You've made it much more complicated than it really is... First off, the Radeon 5450 is NOT better than a GeForce GT220. It's quite a bit slower, see for yourself: http://www.techspot.com/review/244-ati-r... Now on to the general points. All versions of PCI-E x16 are backward compatible... So version 2.0 and 2.1 cards work in 1.1 slots and vice versa.
The particular versions aren't important, because the budget cards you're choosing all have maximum throughput well below the limits of the original PCI-E x16 specification. While the introduction of PCI-E x16 version 2.0 raised the maximum bandwidth, it was like increasing the speed limit on a superhighway from 120mph to 240mph! The higher speed limit is meaningless to cars which aren't capable of going faster than 90mph, anyway.
That's the situation you're in with all cards under $200... the Radeon 5750, GTS 250, GeForce 9800GT, Radeon 5670, GeForce GT220- NONE of them are fast enough to be bottlenecked by a version 1.0 PCI-E x16 slot! You need high-end Crossfire or SLI setups or single cards in the $350+ range for the hardware to actually need a 2.0 slot to run at full speed. As for version 2.1, it operates at the same speed as 2.0 but adds some power management and diagnostic features which won't be fully supported until version 3.0.
Anyway, in order of performance: Radeon 5450 < Radeon 4650 < GT220 < Radeon 4670 < GT240.
The pci-e is pretty compatible. 2.0 will fit 16x slot. If you are running 16 x it'll work fine but won't do what a 2.0 will.
You can get a 2.0 card and it work even if you are running a 16x slot. It will bottle neck it down to 16x though. There's also a pci-e1x that does have a few graphic card but I they are few and far between and I doubt you'll even find on recent enough to game with.
I doubt you will have the pcix you mention also. Just get a later card and you'll be set no agp or pci, just pci-e and it'll work 16x or 2.0. I would also stick to the ati stuff.
From my experience ati is pretty good and nvidea is over rated. Lastly, i'm not sure about you shopping habits but you can hit newegg or tiger direct and get a much better deal than off the shelf from a store.
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