The 'big block' 3.5 straight six is more of an effort to fit compared to a 2.5 twin cam or 2.3-3L from a later E46. The block of the 'small block' inline 6 hasn't really changed in the last 20 years (virtually the same external dimensions), so it is much easier to drop in with minor crossmember mods etc. By memory all that is needed is a sump modification - it wil fit with stock engine mounts.
The 3.5 is also a fair bit heavier, whereas the twin cams from the later E36 on are only marginally heavier and will not disrupt the balance as much. They will more or less match the older big block single cam straight sixes for power, but less torque.
I would seriously stick to the small block twin cam six from a later car. Make sure you check out the BM Auto Engineering website i posted above - they have done E36 M3 engine / gearbox transplants into E30s and they fly...