I've never heard the JL Audio stealth sub in a X5 but I know that our 8" hide away sub system sounds amazing. It will add a lot of clean depth to the audio system, but its not designed to rattle your neighbors windows so if you're into a lot of heavy base then its probably not what you're looking for. But since you're looking at these two setups I'm sure our x108 will fit your tastes.
As for upgrading your stock mids and highs, then it all depends on how far you want to go. If you're going to upgrade your factory amplifier with an aftermarket amplifier then I would recommend getting a set of "off the shelf" aftermarket components much like the local shop recommended. But if you want to stick with your factory amplifier, then our Stage 1 for your car would sound amazing compared to a set of "off the shelf" aftermarket speakers. We've designed our stage 1 speaker system to work perfectly with your oem amplifier and to sound great at the same time.
We replace all 10 of you in-cabin speakers with our Stage 1. We replace your tweeter and mid-bass drivers with Rainbow speakers built to our specification, and the mid-range with a BSW designed and built audiophile grade speaker. We replace your oem .75" plastic tweeter with a Rainbow .75" silk dome tweeter which will greatly improve the clarity of the high frequencies without any harshness. We replace you oem 2.5" mid-range with our own driver which is better sounding and more durable than the oem peice. As for your mid-bass driver we replace your 6" driver with a high quality treated pulp cone 5.25" driver that will clean up the OEM's muddy reproduction of the lower frequencies.
Here are some direct links to both the X108 hide away subwoofer system and the Stage 1 for the X5.
X108 Hide Away Subwoofer System for X5
X5 Stage 1
I hope this helps and if you have any other questions feel free to contact me and I'll be happy to answer them.