I don't really have a budget. I want something loud and clear. I'd rather not give up to much space but would be willing to if I had too. I'd like to keep the RCD, but if something better comes along with Apple CarPlay, then I'd be willing to switch.
Just about any aftermarket radio with apple car play is better, but it won't integrate into the dash as well. It seems a lot of people would rather have the OEM fit and finish over sound quality features, so you're not alone in wanting to keep the radio.
Without a budget, I would suggest going to crutchfield and doing some shopping. It's easy to fit a standard 6.5 component set (some may need spacers) so you have hundreds of choices. I'm running the Illusion Audio Luccent set, they are excellent speakers, but they are severely limited by the OEM head unit. Once you figure out a budget, I can help you narrow your search.
For a sub, are you going to build the box, or do you need something pre-built? Our cars are a little tough for subs, there are some enclosures that fit into the wheel well area to save space. If you don't do that, you can remove the foam around the spare tire to build a box, or you just have to set a box in the hatch. If you stick with a sealed box you can probably get up to about a 12", if you want ported you may only want to give up enough space for an 8".
I think you need to do a bit of shopping so you can see what things cost, and determine a budget. I also think you need to figure out how much space you're willing to give up for a sub, and whether or nor you're willing to buy/build an enclosure to fit into the wheel well, or near the spare tire.