It doesn't really matter which option you go for - but you should try and design out the disadvantages of the option you pick as far as possible.
Cubicle toilets either have sanitary disposal boxes in each one, often making it difficult to enter the cubicle and shut the door behind you (always always place the sanitary box on the same side as the door hinges, please), or they have a communal one in the lobby area which is just grim. They're too small to comfortably change in. If you've gotten all hot and sweaty, you can't strip off to have a proper wash. One large cubicle with a sink in it is a very nice thing indeed in a lobby toilet.
If the private cubicles would all be off one bit of corridor, this could be made into a sort of lobby - especially if it's not a through route to somewhere else. Extractor fans are essential, obv. I prefer unisex if they're private because there's no logical reason for them not to be.
If they're separated by gender, don't do the alternating floors thing - very irritating. And don't put them the wrong side of a security door either. Having to accompany visitors to the toilets just so they can get through the doors and back again is fucking stupid and far more expensive than the occasional laptop going walkabout (yes, I work in a building where they have this arrangement).
And bear in mind that women spend longer on the toilet than men. If toilet provision is minimal, and they're separated by gender, put proportionately more in for the women. I won't queue for a toilet if the gents is free, but it ain't fair on the poor boys standing at the urinal when the girls use theirs.
And don't give hot-air hand-dryers only. If you must have them, provide towels as well.
I'm female and I prefer private toilets. Partly because I just don't get the gossiping in the toilet thang - and I'd be far too paranoid about being overheard by unseen randoms in the cubicles to do it anyway. If you need a tampon, you go and ask a female colleague - they can be found all over the place, not just the ladies. If you need to let off steam you go to the coffee room or the smoking area, where you can see who else is present.
Quite surprised how strongly I feel about piss poor toilet design.
