I'd like for there to be a condom option as well as being able to know if the girl is on the pill. That would make for a more interesting story.

The condom option would be politically correct. I would not want to get infected and would not want her to take me seriously (preggo) when I poked her.

I also think in these day and age condoms should be mandated in games. So players feel more protected.

It's a game for crying out loud! If i wanted to have normal sex with birth control and condoms, i'd call my girlfriend. No worries about STDs either.
As a game there should be far more freedom and less about the worries of STDs and unwanted pregnancies to the point where you'd want a virtual condom.
Condom-less raw sex without birth control is exceedingly rare, and exceedingly hot because of how rare it is (because of the very real consequences that accompany the action). I'd love to fantasy knock up a chick and have them react all scared (or really wanting to be bred, telling you how much she wants to get pregnant, depending on the character/option/situation). Some people even like preggo sex, or at least the visual representation of it.
There's nothing wrong with a condom option or a verbal reminder that the virtual girl you can't impregnate or get stds from is on the pill, but don't use that as an excuse to cut off the more free-wheeling options of unwanted pregnancies, STD risk, or preggo sex if that's how you get your jollys.

It could make for an interesting plot device. Your toon doesn't like condoms and the lady will not have sex without it. Will you take the sneaky path and try to fuck her in the dark, trying to convince her that you're actually wearing it? Or will you convince her to not use one? Perhaps a "bad end" of sorts if you end up knocking her up. 18 years of financial ruin! Mwahahah!

I like the idea of actually getting her pregnant and having sex when she is late in her pregnancy. The thought of "That's my baby in there" is a turn-on for some. Also a option of getting her pregnant against her will can be a turn-on too.

I liked the idea earlier (viewtopic.php?f=6&t=792 shameless self-promotion, sorry) and still do. Especially for the plot thing Malachai mentioner earlier. Also, for the 'infinite story' (tm) pregnancies and STDs would fit very well. Plus, coming accidentally (that is, not when some meter is full or when you press a key) would be another nice mechanic to make the actual sex more interesting.

Dealing with STDs is the last thing I want to manage, so if you're going to have it in, I'd put it in as an option.

Naturally, options for everybody! Especially important in this genre as well. Because forcing ppl to sneak in one level in fps is no big deal, but lets force a gay relationship in one story! At least it will cause quite a reaction... And probly some people to threaten the dev team with violence.