I'd be in favor of adding Joker as a romance sub plot for Femshep for two main reasons.
1) Romantic Comedy Potential
Yes, Joker has fun banter with EDI, but I'm sure the writers could come up with some really sweet-funny stuff, that would be so entertaining that even those who don't normally run a fem shep could be entertained by the dialog.
The "nerd gets the girl" theme probably would resonate with a lot of players, at least, it's a popular theme right now with shows like Chuck, Big Bang Theory etc, and there's definitely that sort of nerdy vibe about Joker.
Plus this would be different then the LI subplots already offered for Femshep (or Maleshep). Alenko/Thane are tragic/emo-angsty, Jacob is tawdry, over-the-top. Garrus comes the closest to romantic comedy, but it still has that built-in angst given the differences between turian and human. So none of those subplots would be the same style as one featuring Joker could be.
2) Femshep ought to be more attractive to the males of the galaxy, Joker included.
Let's face it, the galaxy is designed to make Male Sheps feel not just like a hero, but a big ol' sexy hero in the vein of James Bond or Kirk ....but somehow the opposite doesn't hold true since no male characters (other than the designated LI's) ever really respond in a flirtatious way to fem shep (and only some of the female npcs do, which isn't the same thing anyway). Now I get that the developers might be worried about coding in some dialog/interaction that could offend a large portion of their playerbase, so they're very careful about having random male characters make romantic or suggestive remarks to shep, and generally, anything along those lines seems to only happen after FemShep clearly invites that type of conversation/action. (A standard they don't apply of course to female characters flirting with shepard, since the plot often forces that on you when it involves Asari).
Since that standard isn't going to change, the developers should at least give Female sheps more "safely desginated male LI's" ..or at least some more triggered banter with a male character, and who better then a character that already exists ( since that would minimize the work to animate/code).
A few good lines here and there, even if there's no elaborate cutscene or anything could go a long way to giving FemShep the right feel ...maybe an overheard conversation, or something where you get the idea that even if say Joker wouldn't cross a line by hitting on his commander, he's at least aware that FemShep is an extremely charismatic, attractive lady.
So