I have M60s and haven't hear any of the Axiom bookshelves but been hanging out on this and some other boards for a while and it sounds like you would be hard pressed to go wrong with whatever model in the Axiom lineup fits your budget. The M3's get great reviews and don't need a sub right away, like the super clear but not as deep M22s.
I'll try and take a stab at a few of the easier questions.
Since you won't be getting M80's anytime soon, I wouldn't worry about a high end receiver at this time. M80's have some specific requirements to run full throttle but the rest of the lineup are very efficient. Get one with the basic features you want and put the saved money towards the speaker purchase. Spending extra on the speakers will result in better sound than spending the extra on a receiver.
You can never have too big of speakers, as long as they fit in your room. Just because they are big, doesn't mean you have to play them louder than you would any others. They can be too small for a big room but only personal opinion on the looks decide if they are too big for a small room.
The concrete floors will help a lot with the sub traveling downstairs but it will likely pass through the walls as you mentioned. Unless, the builder has put a lot of money into soundproofing. Still, a small sub played at reasonable levels can still add a lot to music and movies without annoying the neighbors. You just have to be conscious how loud you play it.
5.1 sound for music can be very satisfying with a good source. However, I noticed most of your listening is done from MP3s and CDs. Some CDs will sound nice in 5.1 and many people do convert stereo to 5.1 because they prefer it, but only true 5.1 sources like DVD music and a few others are truly made to deliver exactly certain sounds to certain speakers. Again, for music, I would rather spend the extra money on main speakers for stereo then pick up surround speakers later on as time progresses. Surrounds and a sub are a big upgrade to movies though.
Also, you may find that as you move up to more expensive and much more 'accurate' speakers that the sound of good source material will greatly improve but the sound of poor material will appear to maybe decrease. With M60s I found that the majority of MP3s sounded so bad (because of the compression) that I spent months re-ripping all my CDs to FLAC format to make them sound like the CD again. (FLAC does use some compression but is considered lossless so it is pretty much identical to the CD sound).
M3s, from what I hear, would be much more forgiving to your MP3 collection.
In short, on a limited budget, my personal advice is spend most of it on the 2 main speakers. Spending dollars on the mains gives you more bang for the buck, soundwise, than any other combination. Yes, you will want to add a sub and surrounds if and when you can.
Personal choice on priorities really, better sound for music or more fun with movies.
I've seen some great suggestions if you are willing to disclose your budget amount. Don't worry, most everyone hear started small and built up from there.
