The comments so far kind of say it all. What works for you is best. I have run both mIRC bots and eggdrop bots for years on IRC. Since I know both programming languages it has been, for me, more a question of which language I feel more comfortable getting something finished with. An example, 2 of my eggdrop bots interface with an sql database. I found it easier to code this with the mysqltcl library in an eggdrop bot than in an mirc bot. It could have been done in either language, but for me, based upon the knowledge i had at the time, i made this interface in the eggdrop bot.
Having said all of this, I prefer using an mIRC based bot, only because it affords me the chance to learn more about mIRC.