I agree overall (#1, #2 and #5 are just different views of the same problem, though).
However, there are plenty of hints that the game was more challenging originally. Some of these hints can be found in-game - especially during the final missions - and other hints can be found in the game data.
Take Juni's Defender and the real Blood Dragons, for example. These are higher-level versions of the normal Defenders/Dragons but there is no need for them in the current version of the campaign since you can beat that in a
Starflier or even a
Rhino if you are so inclined.
Also, unless you have flown mission 13 with your eyes wide shut then you should have noticed the empty outer defense perimeter at the The Barrier, and it is a good bet that you have found the un-castrated version of the N***d Interceptors by now ... It could be that the class 9/10 VHF were supposed to be the 'normal' ships for the final missions while the Banshee, Valkyrie, Falcon, Juni Defender and Blood Dragon were intended for people who want more of a challenge (and the Anubis was probably of higher class than 6 originally).
If you want to learn how to fly & fight you could do worse than using a Patriot, Dagger, Defender and Rhino/Clydesdale. With those ships it is easy to find enemies of the 'right size', and the difference between the various ship types (agile LFs, normal LF, HF, ...) is much more marked if you use these ships to fight Stilettos and Sabres than if you use class 9/10 ships. In fact, you could fly around in class 10ers for ages without even learning the most basic flying skills, since there is no need.