Been reading the last few pages ill throw in some of my thoughts. Vanilla android is good but in my mind it's still missing certain features from the manufacturer skins.
I've got a HTC One X currently, Sense is excellent, forget about the launcher and such but it's features make it stand out compared to vanilla. For example social networking, Sense is bliss for this, on Jellybean it syncs high res photos for contacts, it syncs events and birthdays, it syncs your gallery, and friends gallery if you want, all this is missing on vanilla android sure you can use third party apps but this is natively built into Sense and is better than HaxSync for example.
The mail client is excellent. More features compared to vanilla and Touchwiz counterpart.
The contacts management is top notch, probably one of the best on any phone. Android is generally better than iOS in this regard any way.
Sense has burst mode in its camera again missing on vanilla I believe.
Touchwiz also has its own feature set like codec support for native video playback, smart stay, and such. The Note 2 has multi window multi tasking support on its Ui.
Sure vanilla is good but don't count out overlays as they do provide useful features which is missing on stock android.