Eh, I don't agree with a lot of this. Part of what Remender was doing with Apocalypse was building up the character's corner of the X-universe up to match the character's prominence. It rung true to me, especially in light of how Archangel had been approached the preceding years. I also remembered there being a lot of advocacy for getting Betsy and Warren back together before Remender did it. I had no problem with Fantomex, or the debate around the baby Apocalypse situation. Fantomex and his misdirection did maybe end up being a little overused, I guess. I liked the Final Horsemen well enough, though I guess I'll agree Ichisumi could've been handled better.
I think this is just a personal taste situation.
His Cap stuff just never worked for me. Maybe if he'd been paired with somebody other than JRJr.