Now, Having sold over 1500 Uber-Stealth boxes, as I some experience with this issue. I do have some customers who are doing a full blown system, including head unit, amps, speaker and sub. In my 2008 GTI i did everything. I changed the head unit, swapped door speaker with aftermarket 3 ways made just for the mk5 (don't remember the brand, fully gutted the car and did sound deadening under carpet, removed door skins and covered them, you name it.
Now, there are 2 things that made the most difference
1. Head unit - actually ran a single DIN pioneer for awhile in a OEM single din dash kit. I really liked it ad the added power really did make the stock speakers sound better. However, single din interface sucks. I also hated losing all the factory integration. I tried one of the chinese knock off RNS-510, but it sucked.
I eventually settled on a RCD-510 out of a mk6. This seemed to offer the best sound and usability, but this was years ago, so something with android auto may be just as good.
2. Adding a small sub. Now i personally used a 8" in my car, as i am not huge in bass. I did find my having a sub, i could adjust the EQ ( easier with an aftermarket head unit, but doable with stock) to take the bass duties off the door speakers, and they sounded much better.
Key is to tap the front speakers for the sub signal. Rear speaker signal seems to have some of the bass cut out of the signal, and makes it not ideal as an input to the sub amp.
Again, not an expert on everything car audio, but when it comes to mk5 / mk6, i have some experience