You are right, BF2 was an outstanding game, and that is a huge understatement. That doesn't mean BF3 will be, and if anything, going by the recent trend of FPS games, it won't be, and going by the recent trend of DICE, it won't be. Look at the new MOH when DICE got a hold of multiplayer, and then compare it to your older ones.
That main positive here is, as you say, it is designed for PC, and then ported to consoles, the way it should be. Get the best quality on all, rather than good quality for some, and awful for the rest.
And since when has an engine made a game good? It can provide the features, but those are only as good as the programmer implementing them.
I'm trying to be optimistic here .
An engine built from scratch is good because it means they won't have to compromise on the features they want. Another plus is that they already had a test run with the earlier versions of the frostbite engine. Re-writing it from scratch, specifically for BF3 with PC as lead platform is only going to lead to good things.
IIRC, they started work on BF3 not too long after BF2 was released(2006/2007). Since they wouldn't have even had an engine at this point, it gives me hope that the base concept and gameplay of BF3 will stay true to the BF series as development started before the Call of Duty got big enough to influence every game and saturate the FPS market with what we have today.
Plus, I have yet to be disappointed with a Battlefield game in the PC series.