Yes, Thunderbolt can be used to add multiple "intelligent" displays, and in theory at least those displays have (shared) access to bandwidth in the same ballpark as a 4x PCIe slot. (Or to put it another way, a GPU with the same bus requirements as a standard 32 bit PCI slot would only use about 1/8th of the available bandwidth. Or to put it yet another way, the Thunderbolt port on a Mac Mini potentially allows greater expansion possibilities than all six PCI 32 bit slots in an oldschool 9600-style Mac tower put together.)
The reason Apple doesn't make a little desktop/tower is really simple: Apple doesn't think their typical customer needs it and they're probably right. Apple's whole model revolves around appliance computing (and it's getting more-and-more appliance-y every day), and being able to crack the cover is the complete polar opposite of the "appliance" model. Heck, I don't see Windows (or even *nix) users having to pop the tops on their systems very often any more. USB 2.0 is "only" about a third as fast as a PCI slot but that's still fast enough for just about everything that people used to shove in one, so everything from sound cards to video capture devices usually comes in an external consumer-friendly box. Video capture devices in particular are usually "smart" devices these days, encoding straight to MPEG(2/4/whatever), so the only people that *need* a bus-intensive internal device are those with genuinely specialized needs, like working with uncompressed raw HD video streams in a production environment. About the only other common device that really needs more than lowly USB 2.0 is gigabit NICs, and everything Apple sells comes with one. (It's getting pretty rare for *any* PC to include something slower.) Not that many people need multiple NICs, and there are workarounds even if you do need to be on multiple networks at once. (Like using VLAN tagging.)
If you're doing anything exotic enough to really *need* PCIe expansion Apple expects you to buy the Mac Pro. It's expensive, sure, but even *not* adjusting for inflation it's no more expensive than Apple's pro setups were ten or fifteen years ago. In the PC world you can in theory usually make an expensive, exotic card that does "X" work in some cheap rotgut box the local maniac built with his own three hands and save a couple grand... but would that box's baseline performance actually be good enough to do what the card demands of it? There's the rub. Maybe that's what aggravates the "Midrange Mac Desktop" crowd: Apple clearly deliminates its customers into "Pros" and "non-Pros", aka, "Haves" and "Have Nots", while in the PC world everything's a shade of grey. If you don't like it it's certainly easy enough to pick up your ball and go play somewhere else.
Personally the one thing I really *do* value about desktop (or small tower) cases is they usually have the ability to add at least one additional hard drive internally. Frankly, I hate external drives. Except for "pack it up and keep it safe" backup purposes I consider them useless desktop-space-sucking cable-octopus-ing wall-wart spawning monsters, and thus for me at least their reliance upon the things are far larger strikes against machines like the iMac and Mini then their lack of PCI slots. I suppose by extension that also puts me at least theoretically in the anti-Thunderbolt camp, because as well as it might work a Thunderbolt substitute for something that *could* reasonably live on a PCI(e) card will be yet another annoying box daisy-chained into the ever-growing snarl of cables that inevitably surrounds every computer. But on the flip side, in the case of a video capture or audio device that for all practical purposes requires a breakout box for its connectors anyway it in theory might make more sense to just have them on the peripheral itself. Having them spaced out on a well-designed box beats snaking them all under the table and cramming them into a tightly jammed slot cover area. So if you don't mind "dongle clutter" and re-buying your peripherals every few years (and if you're an Apple customer you should be used both by now) in the end it's... probably a wash.