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From the reading the Iliad I see the Trojans & Greeks worshipped the same Gods, spoke the same language and had common bloodlines.  Notable examples would surface on the field of battle on occassion. 

Sounds like Trojans were in fact Greeks.  Having been defeated they fled to found Rome (Aeneas)

If you read the Iliad, the sense that you may have is that the Trojan War was kinda "civil" war. It is very possible that there would have been a strong genetic connection between the Greeks and the Trojans if we don't want to call the latter, pure Greeks.

When the Iliad was written, the pre-classical definition of "barbarian" (varvaros) was not fully defined and formulated yet. There is more then just a passing sympathy of Homer for the Trojans, but nobody calls them "Greeks", although a strong (cultural) connection is not only implied, but vigorously outspoken.

Althouhg, one must note that the Iliad presents the clash between Greeks and Trojans as a sorts of clash between "Europe" and "Asia", so there is a rather firm notion of the Trojans being "Asian", non-Greeks.

I don't know why you brought about the issue of Turks?

As for the "sympathy" I read that in the preface of Iliad. Of course, as a Greek he praised the heroic character of the Danaos but his wailing for Hector and the Troia is the most affecting part of Iliad. This makes me to think in such a way.

On the other hand, why would Trojans ally with other Anatolian peoples against their own kind?

You know in Ancient Greece there were many examples of coalition between some greek tribes against other greeks without thinking about fighting their own kind.

While you're reading the Iliad sometimes you may get confused for some persons whether they belong to the greek side or the trojan. That's because Trojans did have a lot in common with Greeks (names, tradition, religion, language). Nevertheless I don't say that Trojans were pure Greeks (there is no way to find it out) but they may have had a strong connection with Greeks, cultural and maybe genetic.

You can find one of the possible theories linking Trojans with Luwians in my post here.

  http://www.allempires.com/forum/forum_posts.asp?TID=150&KW=perseas&PN=0&TPN=2 - http://www.allempires.com/forum/forum_posts.asp?TID=150& KW=perseas&PN=0&TPN=2

Now, as far with possible links they had with Greeks lets have a look at the royal Trojan's family list of names.

Priam - not a greek name. The only link this name could have with being greek is if we take its Aeolic form which would sound as Perramos.

Laomedon - He was Priam's father name and its surely a greek name.

Hecabe - not a Greek name.

Hector - a greek name, having the same form as Nestor.

Paris -  not a greek name. But Paris had also a second name, Alexandros which is a greek name.

Helenos - greek name

Deiphobos - greek name

Polydoros - greek name...Polydoros was the name also of a son of Cadmos.

Politis - greek name

Laodice - greek name...also it was the name of Niobe's mother in greek mythology.

Kassandra - greek name

Polyxena - greek name

Antiphos - greek name...also this name was shared by a greek commander who participated in Trojan war and was killed later by the cyclops Polyphemus.

now from all these we can have the following final two options..

i) They had greek names,

ii) Their names were changed by bards from foreign to greek.

Greeks adopted their names?

That seems likely in the case of Alexandros, which is a historical name of a ruler of Wilusa (Troy), according to Hittite records.

Notice that the Illiad was so important on Greek culture that surely many people took names from it.

Also, some names could come from a common Aegean background.

I don't think the answer is so simple. What makes a name "Greek" in your list, Perseas?

the Greeknes of the names is derived by their linguistic root and by their meaning. Examples:

Laomedon -  From the Greek words "Laos" and "Medon". This cannot be an adoption or a transliteration, because it is a fundamentally Greek name

Hector - a greek root 

Alexandros -  another composite word: Alexo + andras. Both Greek roots, forming a Greek name with the meaning "defender of men".

Helenos -greek root (probably related to the word Helen (Greek) from the times the Greeks were not called Hellenes but Danaoi.

Deiphobos - greek composite name: By the prefix "Dei" (bi- twol-) and the word phobos (fear).

Polydoros - composite Greek: Poly and doro

Politis - greek root (Polis)

Laodice - greek composite name (Laos + Dike)

Kassandra - this one is disputed as the linguistic root is concerned, although it is adopted as a Greek name even from the Homeric times, especially in northern Greece.

Polyxena - composite name: Poly + Xene

...and so on.

So, names like the above could not (with the exeption of Kassandra) have been "adopted" by the Greeks, because they are fundamentally Greek. I still insist on a common Aegean culture (and maybe even ethnical background, at least partly) of the two people.

Cassandra was taken as slave from Agamemnon. I think you mean Andromache.

From the point that they are mostly meaningful in greek language and their compositions.

For example Hektor is derived from ‘åêôùñ (hektor) "holding fast", ultimately from å÷ù (echo) meaning "to hold, to possess".

Same with Êáóóáíäñá (Kassandra), which possibly meant "shining upon man", derived from êåêáóìáé (kekasmai) "to shine" and 'áíçñ' (aner) "man" genitive áíäñïò (andros).

Its known Greeks had a tedency to regularize foreign names. If we take as example the Achaemenids royal names we have...

- The name Artaxerxes is the regularization of the original Persian name Artakhshathra.

- The name Xerxes is the regularization of the original Persian name Khshayarsha

But on the contrary to the above Trojan royal names, neither of these Persian names have any meaning in Greek language.

Something that dorian mentioned: Homer does praise Hector,but not because of his origin or due to the fact that he is "Anatolian".Homer was an epic poet,which means that he praises the virtuus,the "aristoi".Hector was no doubt the greatest troyan warrior,so the poet could not leave him out of the story.

As for the coming of the Troyans,they couldn't be Greek the way that Spatans,Athenians or the ionic cities of .. Ionia are. The first greek migration is dated in around 1100 B.C., with the coming of the Dorians. The prosperous city of Troy and the war as well happened before the greek tribes massively moved to minor Asia. Perhaps they were a pre-hellenic branch..

Samothrace and founded Troy. The grandson of Dardanus was Tros, which had as son Ilus II (which re-founded Troy and gave his own
name to the city). Ilus' son was Laomedon, and Laomedon's son was Priam. The father and the son of this king, Paris, will be defeated by
the Greeks after raping Hellen (action that humiliated the Greeks and menaced since he would have inherited Hellen's kingdom)."

It is already mentioned in one of the above posts.

Hektor is derived from ‘åêôùñ (hektor) "holding fast", ultimately from "å÷ù" (echo) meaning "to hold, to possess".

The same question was asked of Victor Hanson.  He replied that the Trojans were a Hittite/Semetic peoples and seperate and distinct from Greeks.  But that they shared cultural influences.  His view is somewhat contreversial.

"From archaeological and philological evidence Trojans were probably some sort of early Semitic people and their language akin to Hittite."

I think it's a shame we try to fit all these ancient groups into our neat little categories. It leads to alot of misconceptions, like people envisioning unitary polities that never existed. Alot of groups in the ancient world lay in fringe areas and were hybrid cultures unto themselves, comprising crossover areas from one culture to the next. The Trojans were likely one of these groups, bearing ties both to the Greeks and the Hittites. The Greeks may have considered them civilized and thus would write of them in a different manner than they would of peoples they considered barbaric, just as they wrote differently about the Egyptians than they did about the Persians. As far as naming Trojan deities as Greek deities, well, they did this all the time - they even tried to identify the Hebrew god as Zeus.

The Trojans may not have even been an identifiable, unitary culture of any kind. Homer says that they spoke many languages, and had no common language. Troy may just have been a site that grew due to its trade importance, and different mercantile interests - rather than a unitary cultural or tribal/clan influence - may have been the factor behind its growth. How can we rule out this possibility? I think sometimes in searching for the origins of a people in a particular site, we may be misleading ourselves by thinking there is going to be a single answer.