Resale value should still be good as long as all the mods are tasteful and subtle. Over the top things are what hurts future sales. Buyers usually don't look for heavily modded cars unless it's 16 year olds and usually JDM cars. I love my sunroof. I hate not having one in my truck.
If you can drive an E46 then I would definitely look into it. I've never driven an E46 but that will probably be what I upgrade too. I would prefer an E39 M5 but their still outa my budget. Theirs two twin E39 M5's cranking out 800 and 1,050 go respectively. One is called "El Diablo". The other lives in Bahrain. Both are twin turbos. The E39 M5 has a 400hp V10 engine stock. I was looking on you tube today and their is a number of guys in the UK who have dropped the V10 into an E46!! Sounds phenomenal.
If I had an unlimited cash flow I would do up an M5 for the family and drop a V10 into an E36/46.