In combination with Shoddy Battle (to find a legal IV/nature combination for a particular Hidden Power) and Pokesav (to find out what gender/ability slot a certain PID will produce), you can find these already. Although, any legend that you would need a PID for only has one ability regardless of which "class" is picked, and only Heatran has a gender, which is totally inconsequential in battle for anything other than the never-used Attract.
Yes, as you say Pokesav help you determine what gender/ability a certain PID will produce when the PID is entered on the main Pokemon page and "Create" is pressed; 1st/2nd Class relating to its ability but then the ability would have to be updated manually. Pokesav would therefore actually allow a caught Pokemon with IVs matching the PID to have an incorrect ability.
Furthermore, the applet producing these as output is very useful in terms of hack checking, because for wild non-legendary Pokemon, hackers could get these wrong. This would show up when Nintendo hack tests a player at a tournament, and on some games may show up as a bad egg.
Having these pieces of information as output adds to its usefulness by not requiring the use of additional programs. I just mentioned Hidden Power output as it would make an extra piece of useful information (perhaps could even be used as an input field, along with the options "Fire/Water/.../Any").
I would, however, appreciate a downloadable offline version, but I think X-Act has done a very good job already, and I say thank you for so quickly implementing the gender and ability outputs.
EDIT: To Syberia - sorry for misleading you regarding gender, thanks for pointing out Pokesav 1st/2nd class update to me.