This is a great question. There are many pros & cons on both sides.
I would definatly make sure the EA was MPFI, as others have said. Trust me
I have just gone into a GLi EBII from a CFI EA and as you say the EBII is more refined.
I find the ride of the EBII is much nicer & with a few minor adjustments to the suspension
I know it will ride even better.
Although both of mine were autos I know there is a huge change from the 3spd to the 4spd boxes. I would prefer a manual but as you say there harder to find.
I havent been in too many other MPEI cars but the feel of the power in the EBII is amazing from what Ive been used to.
So my thoughts would be this .......
Think how much each of these will cost you to buy. I would expect the EA to be cheaper.
Think about how much you will be then left for any mods that you want.
Think about the age of the cars & how much wear & tear has been done and what will need replacing & what parts are easier to get.
Remeber the older the car the more that can go wrong......... If you are after a long term car then I personally would go the EBII ........ Gear Boxes can be changed after all