I went for Reckhorn D-165 which are 6.5" sub woofer drivers that work well in small enclosure. On paper in a 6L sealed enclosure the -6dB frequency is 50hz with a correctly designed port they can go down to around 35hz. They are around £30 a piece, I haven't installed them yet, but from a construction perspective it looks like very well engineered German engineering.
In lots of ways I had the same dilemma as you I wanted to improve the sound of the Z4 without it costing the earth (the law of diminishing returns applies on a Z4 IMHO). A key decision is what you want from the cubby box speaker. I decided that I did not want a full range speaker for two reasons: I don't like audio coming from behind my ears i like ideally two point sources in front; any mid to high range frequencies from the cubby box behind the drivers seat are unlikely to reach your ears, the seat will block them, but you will hear the one behind the passengers seat. I don't like such a soundstage.
So my requirements were simple i only wanted a sub woofer in the cubby box. Like yourself I was also interested in fitting a 6x9 speaker (I also looked at 7x5 and 10x7) but when I did the maths on the speaker parameters I could not find one that would give sufficient bass (thats not to say they don't exist, I just couldn't find one). I found many 6-6.5" sub drivers with a good calculated bass for a 6L enclosure (I even found some 4" that worked well theoretically and considered doubling up). I settled on the Reckhorn because it comes from a manufacturer with a good reputation for quality audio and it was much cheaper than the competitors.
It is unlikely I will get them fitted soon because I need to do a lot of work on my garage, but hopefully by spring i will have them installed and can give some feedback.