Great cars overall. We have an R53 model - 2006 S with the 6 speed paddle shift automatic trans.
Generally speaking, the newer the car the better. Some small improvements over the years with regards to power steering pump/fan, supercharger internals, passenger side motor mount, front struts and other odds and ends. I think the 2005+ cars got all of this.
The thermostat housing is made of plastic. I would think that by this point most [of the housings] have been replaced under warranty once they start leaking.
The passenger side hydraulic motor mount tend to fail. I'm on my 3rd. The first two didn't last longer than ~15-20k miles each. The 3rd seems to be holding up well. The aftermarket co Texas Speedworks has finally developed a replacement motor mount that is not hydraulic. The word is still out on NVH.
Front lower control arm bushings are replacement items. Replacement interval varies according to road conditions and usage. So far, only the driver's side lca mount has gone on my car at ~50k miles.
The stock sport suspension is surprisingly good. The shocks are actually quite nicely damped and stock spring rate is a good compromise for DD and spirited weekend romps. The suspension is travel limited so lowering springs compromises ride quality. Stock shocks feel great after 55k miles of CA roads. We now have Koni Sport Adjustables and they feel sportier and livelier.
For a DD, 16" wheels and non run flat tires are an excellent compromise of looks, sportiness and comfort.
There have been some reported cases of superchargers failing on high mileage cars due to the supercharger oil being consumed. The oil is not readily serviced w/o removing it from the car. Some hypothesize that this is aggravated by smaller diameter pullies running the supercharger outside of its efficiency range.
The Mini aftermarket doesn't seem very experienced. A lot of first time modders out there with little understanding of what works. I'd favor a stock car over a modded car as a result of all of the above factors.
We don't ever plan on selling ours.