From what I understand the stock system isn't bad it just has no sub so you are forcing speakers to do an additional job which they were not made for. Add an amp and a sub and I bet it would sound pretty good. A lot cheaper than DSPs and all that stuff.
This is true, but you can't just add a sub without adding a signal processor or converter to take that bass from the doors and direct them to the sub. Otherwise you're just adding more bass and the door speakers are still stressed doing the same work. Instead of something like a 2 channel+sub converter like an LC2i that isn't going to remove bass from the doors, you can run the LC7i and a 5 channel amp. The LC7i is going to have a crossover to move bass frequencies to the sub output and away from the doors. That is more wiring to do that, but the cheapest way I know.
Okay I lied, you can just put "bass blocker" caps on the factory door speakers to limit bass frequencies to them. That's ultra cheap and would work. Then you can run an LC2i and only add a sub and amp for the bass you took out. Just a bit more "bandaid" feeling than I like.
The Helix system on the other hand takes all 4 speaker outputs, runs them through an EQ and time corrected DSP that was designed for VWs, then spits out 4 new speaker outputs with more wattage than the OEM amp and sends bass frequencies to the Helix sub. It's very effective at what it does and sounds great, plus you don't have to modify anything to install it.