Yes you're hearing a mismatch of efficiency. I had a Hertz HSK 165, similar quality, and listened to one side in first. I gaurantee your highs are 10 times better but you don't hear it. Your factory BA are thin near paper speakers with no crossover. Do the pair and then throw in a CD. If you think Focals sound worse than stock then you must be listening to MP3s at high compression and you're finally hearing what garbage sounds like clearly
You'll be doing an amp soon. Also, with those speakers set your EQ back to 0 for hi, mid and lo.