OP, your not really comparing like for like?
Only you will know how you use your estate - if you frequently carry more than just a small load of luggage (ie: never use the additional 'window' space and keep everything under the luggage cover) then you 'may' be able to cope with an E90.
The boot in the E90 is quite large, but you are used to a large boot opening, as others have said, the E90 is quite narrow with the boot open, sayiong that though I have fitted 2 largeish suitcases in mine before with no bother. I am taking the missus and 2 kids to France in it and have purchased a roof box to carry all the lighter kids crap (buggy, footballs, food, etc...) and keep the boot for the cases.
I got an E90 over a coupe, because the rear doors were essential for me having a small baby (cue the 'I fit kids in my coupe OK' posts!!) - the M3 gives me a sports saloon that not much can keep up with when I am driving alone, and a practical family 4 door when I have the wife and kids in tow.
Also factor in increased running costs, (slightly more expensive servicing, tyres, fuel economy, etc...). Oh and the modding bug may bite, that costs even more money
