I doubt that they'll make Kira a bad guy. I mean, in Gundam ACE polls, Kira rank the top of Top 30 Male Characters for few month. I'm not sure how many month.. but I think after Archangel left, and Kira gets more screen time, his rank already outdo Char, Athrun and Shinn. Yes, even last month polls Kira still at the top. So, if they made Kira a bad guy in the sequel (IF THERE IS ANY), there's two thing they have to face. The drop of rating and the wrath of fans. Believe me. The drop of rating means there will be no more sequel. Compared to SEED, the rating for Destiny is really BAD. Much later after Archangel left ORB it's get better... and only after Phase-30+ it's get more rating. So, there's a possible of sequel. But from what I read at Gunota's in last August, they intend to made Kira & Athrun the main characters IF THERE'S a sequel. Well, it's only a rumour.. but the one whom said that is actually a BANDAI staff. Here's the quote from Gunota's [on 15 August entry].

Again take this with a grain of salt.
The following blog has a report/dialog between a customer, store owner, and a Bandai staff member during a Bakuseed (miniature electric motor car) tournament. That, of course, makes this report hearsay but still of interest as far as possible commentary on the state of Gundam at the moment goes:

The Bandai staff member commented that currently DESTINY as a series is unpopular with ratings on a downward trend (see below for that) and merchandise not selling well including Gunpla (something also mentioned at Plamoya-san's Useless Diary). The store owner adds that Bakuseed is outselling Gunpla at his store. The conversation switches to a possible sequel after the customer said "I guess no sequel then. Wanted to see one." The Bandai staff replied that they are currently exploring the idea of another SEED sequel which will again feature Kira and Athrun, concluding a SEED trilogy. The ending of DESTINY will be made so a possibility of sequel can occur. If it were to happen, they won't be doing it until after next year as time slots are all filled up for the 2006-2007 lineup. It is currently set as a trilogy, however more sequels will be made if proven popular.

Again, I must say it's only a rumour. Still, it's much better than the ETERNITY crap. ^_^ If you ask me, I'd rather believe Gunota's.. since they've reliable source...

as long as there's hoshi souichirou i would watch it and i'm super glad for koyasu takehito, but where's Kira and Lacus?!?!?!?!?! TAT
Would be nice to bring shinn back (as kira's apprentice lol), now if it's really true, i am just watching this for my fangirlism

most of the time, the staff would officially annouce the new season three months before the real release date, GS eternity might just be a rumour