My biggest issue with Eclipse Phase is that you spend all those resources making your morph awesome and at any moment you can get put into a new morph for one reason or another and suddenly you suck. 
A good portion of the system needs to be streamlined. Chargen is a giant algebra problem with the choices boiling down to "are you taking these skills y/n," the entire hacking system needs to be rewritten, morphs and aptitudes are a giant mess, combat boils down to who shot first with the giant weapon in the one weapon skill they specialized in (and there are like twelve of the damn things) unless there's a critical fumble, etcetera.
Also, your aptitudes are going to be sort of counterintuitive, because if you want to make the most of your skill points you're going to set them high on whichever aptitudes cover the most skills you want and then tank them everywhere else.
But if we keep talking about this, we might need to split this thread off.
