Yesterday i tried to do a fresh install because i had some problem renabling everything.
To my suprise i noticed there was huge differences between my last version updated always with magento connect and the fresh install(with of course the data reimported).
1-Speed.The fresh install was much much faster even with cache disable as before.With cache enabled it’s awesome.
2-Forms.There are many forms that has changed but they weren’t with connect.For now i noticed a new setting in the cache and a different backup form,but i am sure there are others.
Please notice my upgrades have been always ok,never had any problem reported by the pear installer.
My paypal pro settings were also screwed with the fresh install so i think there was some changes in that part too.