Well, I'm pretty much over Guilty Gear so the fanboyism is gone, and I own a 360, so I might actually be able to give a unique perspective into this question. I hated Overture when it came out, so, here's a few reasons.
1: Daisuke's handling of it. The way he said 'it's the game GG was meant to be in the first place' and the way he struck X onwards off the canon, was basically a complete "fuck you" to the actual current GG fanbase.
2: The characters. The only decent one (imo of course) was Sol, who really isn't that decent. Other choices? Generic sentient-weapon loli, two furries, two crossdressers, and I think they added Raven later right? GG's always had very eccentric characters but there wasn't enough for many people to find the kind of eccentricity they liked... Also in a cast of 7-8, 2 furries and 2 crossdressers is 2 too many in both cases.
3: The two genres (3rd person fighting and RTS) really don't mix. The RTS players generally want to have a big war, and the fighter players generally want to have a one on one fight. There are only a handful of people who are happy to play one of the fighter type characters and take on hordes of buffed enemies while the opponent plays keep-away, or happy to play the RTS characters and be mauled if the single player unit manages to get close to their own player unit. You COULD just play for the chance to fight people 'playing the same genre,' so to speak, but there were too few characters for there to be any diversity this way.
4: The fact that most GG players thought (and were right) that the creation of a 'proper sequel' in this style would mean the end of the fighting games. Boycotting it added a chance that Daisuke would drop the spinoff project and go back to fighters.
I've said this before and I'll say it again; I'm sure Overture is a fantastic game if you're in the right niche, the same way GG was a fantastic game if you're in the right niche. The only problem is that it wasn't the same niche as the old games, thus erasing the entire 'guaranteed' fanbase, and the stigma around it made it too unattractive to a new fanbase to find its footing.
The game would've had a much, much, much higher chance of succeeding, if it had absolutely nothing to do with Guilty Gear. Daisuke's insults and insistance that he have his baby and that his Mary Sue lived on had a huge role in its inability to succeed.