I've currently got a 3 door mrk5 GTI (as thought it looked nicer at the time) but have a mrk6 GTI 5 door on order reason being now we have a little one it's a nightmare getting her in \ out of the back of the 3 door.
The sliding front seat is a pain in the backside as over the last 3 years the cable or clip or something that allows it to slide forward when you pull the handel keeps breaking every couple of months. Has anyone else had this problem (guess if you're in\out of the back all the time it's more obvious!)

Key differences I've found (if you have youngn's aged about 2ish):
3 door front sliding seat system keeps breaking, then you have to manually push the seat forward (if you know what I mean using the leaver under the seat), as well as pulling the handel to move the back of the seat forward.
3 door rear window is higher and smaller due to car lines, so less for the little one to see out of, even though the isofix seat is high up she's only young.
3 door doors are too big especially in car parks when trying to get the little one into the back.
3 doors are a nightmare if your out with your mates and they need to get in \ out of the back (especially if one of them is a femail with a skirt lol)
Regarding 5 door new GTI:
5 door was way easier to get little one in \ out also the door opening is a good hight so we don't bang her head getting her in (the MAXICOSI isofix seats outstanding and safe, but have a large base so are high up). I actually tried a merc CLS and almost had to fold up daughter to get her into the seat the door opening was so low in the back!
5 door window is larger for little one to look out of, plus very nicely tinted so no need for binds
5 door is way way way better in car parks with small bays
5 door is ideal for nappy changes if your in the middle of nowhere or a pub with no changing facilities (i.e open back door and put changing mat on back seat, can't do that with a 3 door).
My thoughts:
Wife drives the GTI mostly, but we both got so fed up with the 3 door that have put an order in for a new mk6 5 door GTI (as I've got another car I use in the week with 5 doors so can see the difference).
Also having a larger second car is only part of an answer (i.e tricky to take them both on holiday to wales, for example a Q5 has loads of room and is very nice etc, but you would miss the GTI fun on the roads when you get there and have off loaded all the baby stuff etc!).