I now definitely take tyre/mud clearance into consideration as my current bike has little of either. I guess for XC tyres as intended it's OK, but put anything bigger than a 2.1 on and it all gets a bit tight.
Potentially bottle bosses. I am thinking of getting my Lumi battery bag swapped over to a bottle as the bag has really knackered the paint on my bike in the 2yrs I've been using it. The thought of doing the same to a brand new bike has got me thinking about getting it changed. BUT, the Zesty (on my shortlist) doesn't come with bottle bosses…..hmmmm.
Non-standard stuff that might be difficult to get hold of in the future. Not sure if this is irrelevant or not, but the Fuel EX for example; does the ABP require a non-standard QR for the rear wheel? Not sure, but if it did, it would put me off a bit.