These are sorta spiritual successors to Master of Magic right? I got that off GOG a month or two back and loved it (never played it back in the day), a newer game of that style would be great, the AI in MOM didn't seem to do much in my games which was a shame...
They are inspired by MoM in many ways but they are quite different.
1) Is Shadow magic the best one to get if I only get one (mostly due to lack of time to play them all)
Either get Age of Wonders or Age of Wonders - Shadow Magic. (AoW Shadow Magic is an improved version of AoW 2)
Both games are great, my personal favourite is the first. Many people think the first is best end even more prefer the third. There are many differences between them.
The artwork in AoW 1 is of a lower resolution than in AoW: SM but I still think it is best in the first. If you have the time look at some videos for both games and see which one that appeals to you the most. You can't choose wrong anyway.
2) Does it still play like Fantasy Civ (from what I saw it looks like a HOMM style game)
The AoW series is not a fantasy Civ since the main focus is on war (on a strategic and tactical level) and exploration\exploitation. City management is basic in AoW 1 and a little more involved in AoW 2\SM. There are many different things to manage like magic research, heroes levelling up, upkeep for your army, the movement of your troops (they can move on their own, they are not confined by heroes like in HoMM), control over the important resources on the map, racial realtions, diplomacy and more.
It has many similarities too HoMM too but it is a much deeper game.
3) same style of battles as MOM? (that seemed to handle stacks much better than any civ I've played :) )
Different from all those. The battle takes place on hexagonal map that is representative of its location on the strategic map. Each unit is represented and can act individually (they are not stacked on the battle map, so that suggests that each unit represent x number of soldiers.) The battles can get quite large and epic. Up to 56 units, though there seldom is more than 48 involved. The sieges are great with walls that must be torn down (some units have other ways to pass the though) and many tactical opportunities for both the defenders and attackers.
In AoW 1 you need battering rams, catapults or some special units that are allied with certain factions like Giants that throw boulders to bring down the walls. In AoW 2\SM any unit an do it.
Most of the units have many passive and active abilities that can be used in battle.
4) Does it still have overworld/underworld planes?
In AoW 1 there is one overworld and two different underworld planes. In AoW 2 One overworld and one underworld. In AoW: SM there are One overworld, one underworld and one shadowworld (different dimension).
5) Are there still Lizardmen? :)
Only in AoW 1. They are great though.