AGP is alot faster than PCI 1x, and only old cards use that now.
AGP is alot better, and don't worry, I still have an AGP slot and I'll have mine for a while
Even though that second card is better though, the speed difference won't be that immence just because you've swapped slots since its the card mainly that has to power what gets sent to the slot, and its only 1 up.
It should be a bit more powerful though I'd think, but how powerful? I couldn't really say I'm afraid.
THE SECOND CARD:
The Second card, even though its not the same make (doesn't really matter), I have a link with a few things about it:
Now, its a Direct X-8 card so with a game like BF2, on low settings, you'll be forced to run at the previous version (The new is Direct X-9) and so, you won't see any of the advanced effects expected, but this shouldn't be a problem.
CARD I'D ADVISE INSTEAD:
I advise you go for a card like this: (Remember, Link is only for showing purposes unless you live in the UK. Its a good store I think)
Its only a tad bit extra cash, supports Direct X-9, and also has 256Mb of Memory for textures in games, and will run BF2 better than the one you picked, and many more games also.
Trust me. With that card, you'll definietly notice a performance gain from your old card.
WAITING FOR A PCI-E:
Since that card doesn't cost that much, I'd go for it and thenn save up for PCI-E when you want. Its not exactly a thing you must go for. Its just that all new cards will use it.
Plus since you've just got hold of a new AGP board, theres no point throwing it in the bin. It'll b alright