Where do you live ? A lot depends on where you live and are going to register it as the MK VI is a later car and cannot be registered in CA. Also there is a good chance it is registered as an older Mini so may be a problem in other States presuming it is not in your home State.

You will get as many opinions as there are people on this board.  

Were this my decision I would base my decision on how I plan to use the car and where I live.  The Mk2 is going to have sliding windows.  That's a lot of charm but not much ventilation if you live in a hot climate and plan to drive the car regularly.  The later car has a lot of go-fast bits.  Keep in mind that the 5 speed is not a factory gearbox.  Others will have to comment on the availability of parts.

If the Mk2 is an S and not just someone's 1275 conversion, that would be my choice as I just drive around town.  To me, an original early car is always worth more.  If were planning on spirited driving and/or highway driving, the later car with the 5 speed might be more comfortable.  If the later car sounds like what you want, it is almost always less expensive to buy someone else's project than build your own car.  

looking for my first classic.
i've been debating though, should i get a stock classic or just go for a full upgrade?

at the moment, i'm looking at a 1969 austin MK II 1275 dual carb and an MK VI with a 1300, weber 40 dcoe, 5 speed, gaz shocks, hi los, kad calipers, 3pc wheels. Both have all service records. Asking price are similar but nothing concrete.

this could be a no brainer for some but a tough decision for others. Like me.

if the MK II could be purchased at a decent price, would it be a more desirable classic?
or should i just go all out on a completely gutted car?

just need some inputs.

thanks.

im excited for my first classic!