Well, part of that cost is install. So if you feel like you can pop off some panels and give it a go yourself it's worth a shot. Second you are paying retail. there is a mark up on those components. you are going in blind and getting the recommendation of the store. there is a cost to doing that.
I suggest you start with just swapping speakers. You may find that doing so will make the system sound better with just that. While I am not a Focal fan, they are not bad speakers.
What are your sonic goals
What type of music do you listen to?
Does the 9th Gen Honda you have use a volume dependent EQ/signal processing to reduce the amount of bass the louder you turn it up? You may want to ask the shop.
Without knowing your tastes, goals and listening volume, it's hard to actually recommend something and end with you being happy and satified with the money you spent.
heck, a lot of factory systems especially a 4 speaker set up lack umph in the low end. Sometimes just adding a small subwoofer and amp/powered sub is enough to take the load off the other speakers and you can enjoy the factory system.
For your average car audio person, I usually suggest these steps. Granted, I usually research the car a bit but we will just go with the steps for now.
1. Add a subwoofer and an amp or a powered subwoofer (sized based on what the person is wanting.)
2. Replace the front speakers to usually a component set woofer and separate tweeter with a decent passive crossover.
3. change out head unit or add a signal processor if the factory head unit is a PIA or uber integrated.
4. Add an amplifier to power the cabin speakers.
Now, you can combine 1,2, and 4 pretty easy and cheaply. Buy a 4 channel amp. Bridge channels 3 and 4 into a mono channel of decent power and power the subwoofer. Use channels 1 and 2 to power the front speakers.
Or a 5 channel that will drive all interior speakers AND a dedicated channel for a subwoofer
Subwoofer for the five channel amp
Subwoofer for the 4 channel amp
Basically same subwoofer just different coil configs.
You honestly will not find a better sub for the money that works fantastically in .7 cubic foot (that's point seven) ported to 30 hertz. heck double the money and it won't be better. Clean distortion free uncolored bass. You can go cheaper for sure. Look at kicker/Fosgate/Alpine/Sundown etc... I canthrow out some examples if you want.
So to show you how I would budget
JBL GTO speakers
~600 bucks after wiring kit and simple sealed enclosure not counting if you have to pay for the install
Rocking system that should blow the doors off the stock one (rounding prices)
Polk or Massive 5 channel at 300
ID speakers or the JBL MS at 300
Dayton DVC HO subwoofer or if you want more, 2 of them gives you even more low end support
4 gauge wiring kit
~1100 bucks + install
Or any other combination you can think of. I just threw out some brands i am familiar with that won't break the bank. Sonic is a great place to deal with. look at Amazon as well.
Sorry if I overwhelmed you...