The problem with mixing regional and local services in the same franchise (with both FNW and ATN) was that they did unit swaps and finished up sometimes putting 142s and 144s on long distance services. ATW do similar now with 150s on long distance and 175 on short distance
Before, if there were no long distance units (e.g. 158s) then the operator (e.g. ATN) had to put a "local" train out instead (such as the Pacer you refer to).
Now, if there's no long distance units (e.g. 170/185s) then TPE just cancel the train.
I don't think anyone would claim a Pacer were suitable for a longer distance route like Transpennine, but if it were substituted only when there was no other stock available then are you saying you'd rather the train were just cancelled?
As for changing boundaries etc, a lot depends on electrification plans. For example, the planned electrification of Manchester Airport - Glasgow/Edinburgh services means that they are better "bedfellows" with the West Coast services currently provided by Virgin.
I think that TPE and Northern will be merged back (with parts sliced off to EMT*/ Virgin etc), which is no comment on TPE/ First/ 185s, but realistically a TOC with only 60 trains covering an area from Glasgow to Cleethorpes/ Newcastle to Liverpool is never going to be very efficient to run (depot sizes etc). However there are then questions to ask about whether TPE North could fit with XC and thats a whole can of worms...
...but, in general, it makes sense to have one operator running local and "longer" services, encourages co-ordination, keeps bureaucracy simpler... look at the muddle in Lincolnshire where the re-jugged ECML services (East Coast) don't connect with the local trains (EMT) - compare that to FGW's ability to co-ordinate the former Wessex services with Paddington HSTs.
* - the Cleethorpes service has nothing to do with the rest of Transpennine - giving it to EMT/ Northern is a no-brainer.