I am about to relocate from Phoenix to Malta. MLA will be my new base for what look like many years, if not for good. The company I will work with only flies economy and in the beginning it will not be much flying but since that will add up later I would like to get a jump on a good program.

Let's talk routes.. The following routes will take place once month each;
MLA-LIS
MLA-FAO
MLA-NCE
MLA-CDG
MLA-OSL
MLA-BGO

Other random flights that I am aware of at this point;
MLA-BZE
MLA-SOF
MLA-KBP
MLA-PMI

Also I guess I would be going home once a year or so; MLA-MIA

So there it it, any suggestions to what European program I should focus on? On board service is important so is lounge access for delays..Also when flying alliance metal..

I have traveled very little internationally, how do carriers over there compare to what I am used to on UA and US? Is there someone that sticks out?

Who would be my best bet? Thank you for reading and any info and input you might have.

You would probably do best to choose a program whose European partners offer the best connections between Malta and your European destinations. I'm not familiar with Malta flight schedules, but the UA program might be best, because of its partnership with LH, LX and OS. There should be reasonably good connections at FRA, MUC, VIE and ZRH. You need to be careful, however, since some economy fares now earn reduced mileage (or no mileage) on UA.

If AB flies from Malta to Berlin or Dusseldorf, the AA program might work as well.

I'd probably go for Miles and More (LH,LX,OS etc).

The primary reason is that they are one of the few programs that allows you to credit flights from Air Malta (by far the biggest carrier at MLA), albeit only at certain fare classes and for fixed amounts. Still, this would help you earn something when a non-stop is important to you.

When connecting, Lufthansa is one of the few alliance carriers with year-round service to their hubs (FRA and MUC), from where you can reach most of your destinations easily (BZE will require another stop, likely in the US). You could also try AZ via Rome or AF via Toulouse, but they don't have the Air Malta agreement nor as wide of a connection base as LH.

In general, the European programs won't be as generous in earnings with discounted economy tickets as the US programs with which you're familiar, but even 25% earning is better than nothing. So I'd lean towards M+M, unless you wanted to just disregard programs altogether and go by price, which might not be a terrible idea in this situation given the seasonality and diversity of airlines that serve MLA.