In terms of immediate need, the Delta Flyer came to be because the heroes needed a batyscaphe - a craft capable of diving deep into the atmosphere of a gas giant. Tom Paris just had some tangential fun when completing the construction work.
How did the DF do better than standard shuttlecraft in the pressure resistance thing? Was it a stronger hull (future materials might well suffice for that)? In that case, an all-new craft would be much better than any attempt at modifying an existing one. But if the trick were done with forcefields or structural integrity fields, all they'd really need would be a craft that could accommodate the required magic field generators - a good excuse to go for the Aeroshuttle, as its only known quality is its runabout-like size, at least equal to that of the DF, and probably a tad better.