I do hope the 323s are not replaced by 331s, as 323s are much nicer than 331s.
They aren't, and I say that as someone who will happily admit they have a soft spot for 323s.
331s have a more comfortable seating layout, more pleasant lighting, air conditioning, better luggage facilities (especially now that the subfleet of 323s with additional luggage racks have had them removed), less noise in the saloon, wider doorways, faster acceleration and a higher top speed, plus they still feel very modern. The 323s aren't ancient but are showing their age a bit.
I think 323s are more than adequate for the job at the moment, but unless you judge the train solely on the uniqueness of the noises the traction motors make, it's hard to argue that a 331 wouldn't be an upgrade.
If the 323s are to be replaced by new trains something purpose built will be needed (aka not 331s).
I don't think that's an issue. 331s are already seen on routes that used to be operated by 323s (and 319s, which have a similar configuration inside), i.e. Manchester Airport, Hazel Grove, and occasional appearances on Stoke, Crewe and Hadfield services. They seem to do perfectly fine.