Well currently all modern boards use pci-e 2.0/3.0, and at the moment 3.0 has no advantage really and all graphics cards at the momment are pci-e3.0 and are compatible and the case that comes with the ibuypower one is a nzxt case and is a standard case compatibility is always basically guarenteed if u match the motherboard and the case as in lets say a case is compatible with atx, mAtx, mItx, well then u can put those three different form factor boards into that case and expect full compatibility with the case mount and front panel hook ups, but u will not be able to do extended ATX, XL ATX, or something like btx and utx.
again at the current moment match the motherboard u pick or cpu u pick to a corresponding socket like LGA 1155/1150/2011 for intel or AM3/am3+/fm1/fm2 for amd and of course after u find a board or cpu make sure that the board will support a certain processor, for amd certain boards wont be able to use the 125watt processors or even at all if there isnt a bios update or cpu support list for that cpu. To figure out pick a board with the features u want with good reviews and meets ur needs and then if its not a cheap $60 most likely it will b able to use almost all cpus that has the same socket, same for upgrading an existing pc. But in the future more than 5 yrs there may not be as a big varierty of lets use ur example of upgradable cpus that will fit the motherboard for lga 1155 and beats the i5 thats in it.
RAM is a easy pick, pick the upgrade speed u want and the brand and quality and just make sure its for this generation is ddr3 or for older pcs ddr2/ddr, and for future boards ddr4. The motherboard has the specs for what memory is compatible.
So lets take the ibuypower pc, it has a i5 3350p, could upgrade to a i5 3570k or i7 3770k as there the best cpus for that gen i5/i7
upgrade the psu to a quality psu with possibly higher wattage standard atx which majority of all cases use
Graphics card to something like a 670/680 gtx from same generation or newer 770/780 gtx, or amd 7950/7970. Use benchmarks to compare and see whats better or get another 660gtx and run sli if the board has two pci-e ports
Add a Sata III SSD of ur wanted size for faster boots and loading speeds or another hard drive
Update the current 8gb 1333 ram to a higher speed like 1600-2133 and 8gb-32 but high ram freq usually require a OC and 8gb is more than enough for gaming but u can get 16 or more if the board supports up to 32 or 64gb
You could take everything out of that nzxt case and throw into ur own choice of a ATX case.
All this info is easily found on the motherboard specs for compatible cpus, ram(size,quantity,and support), sata ports, pci-e, form factor.
And after that the case u pick will show in specs its form factor and all the motherboard form factors it supports and most use a standard ATX psu unless specified.
A little research and making sure certain things match will get u compatible upgrades, and alot of things dont have to deal with what can do into the tower (case) as the case houses everything it just needs to fit the motherboard and psu and the dedicated graphics card for its length and if u add one a cpu cooler.
This all seems like alot but for me its seems like common knowledge lol and a little difficult to put into words