I would use DDR2 RAM with an i.MX253, preferring it over mDDR because of lower costs. The problem is the limit to 4 banks memory,
so basically a single chip cannot give me enough memory.
Is there some way to allocate more DDR2 memory, other than use both
the CS lines of the EMI (max two chips)?
You can ground the BA2 on the memory side, thus you would be sparing half of its size, but this enables you to use more memory per CS. For instance, if you use a 2Gbit device, you would be able to access 1Gbit which is more than the 512 of the 4 bank devices...
Besides this option, the only other possibility I see would be to use the second chip select.