I think you got most of it covered except for living materials, which can’t be replicated because of the resolution limitations of replicators - like cargo transporters they operate on molecular resolution instead of the quantum resolution required for live transport. Gagh is a good example; because it ideally needs to be live it can’t be replicated in its intended serving form but has to be kept in barrels in cargo.

The other limitation would be stuff that’s prohibited by program not to be replicated, like weapons, banned substances, although that’s of course a coding issue rather than a materials issue.

Also, to correct a common misconception/inaccuracy repeated above - replicators don’t convert matter to energy or vice versa. They operate by dismantling the raw material for replication like a transporter does then reassembling them in new forms. The underlying technology is the same as the transporter, except that it rejigs the matter stream into a new configuration.

Which is why the question as to whether you want a holodeck or a replicator strikes me as a bit off because replicator technology is part of the way holodecks work. When you eat food on the holodeck it’s very likely that it’s replicated food, not a hard light illusion. Holograms of people can also either be hard light constructs or meat puppets manipulated by force fields, depending on the program and its requirements.

So if you ask me - holodeck or replicator, I’d choose holodeck because that gets me both the entertainment value and the ability to make objects and food.