First of all I would like to thank MajorJuggler for making all of these house rules.
You're welcome! The game has changed a lot since I have last added anything here, but I'm glad that someone still finds it useful.
I have decided not to publicly release MathWing 3.0 or the associated balance fixes that result from it, so I have been intentional about not updating this thread. The House Rules here were done using MathWing 2.0, so while the changes are generally pretty good, there is still a lot of room for improvement. So feel free to tinker yourself, these changes aren't a golden standard or anything.
Second is there a way to fix a ship without simply lowering its cost (titles, mods, etc.)?
Absolutely! This is the approach that FFG takes to fix underpowered ships, and it can work well when done correctly. My approach here is to tinker with the underlying mechanics as little as possible though. It's purely a philosophical approach of staying as close as possible to the designer's original intent. Generally speaking, every ship and pilot can serve a viable role, but its points need to be priced around what it is worth.