I 've done several posts on the "Any owners yet" thread about our experiences over almost 4 years with my wife's Mii. We originally looked at the Up! and Citigo but this was available pre-reg at a good price with decent spec.
No fundamental differences, the seats are the same even on the Gti, other than trim pattern. Some say the Up! has better soundproofing but I've driven a few and not noticed. You'll be aware of the differences in grille, rear window (and side window on the 3 door) which are a matter of personal taste.
The Up! does have a better choice of engines if you need more power, 90ps and 115ps (Gti), in addition to the 60ps and 75ps to be found in the Mii. We have the 60ps and it does the job perfectly well, very nippy in town, cruises fine at 70, returns around 50mpg in normal use (My wife only drives short trips). I have used it for a couple of 250 mile round trips up to Northumberland while I was between cars, and it coped ok, mid 50's mpg, though care is needed for single carriageway overtaking.
The Mii is not that popular on here (this is seatcupra.net after all!), but there are very helpful forums which have members with all 3 marques on
www.upownersclub.co.uk and
www.briskoda.net which are well worth a look.