Hi, I also say try it out first and see what you think. The Mags might not be the ultimate or pinnacle of portable lighting, but they are quite usable and affective.
I've not personally tried a factory Mag LED light yet, but recently I bought a CREE XPE drop in for my old 6d MagLite, it's rated at 180 lumens at the LED and I have to say it's transformed the flashlight. It's highly usable and while brighter would be cool to have, I've not found I've needed it brighter for what I use it for.
In terms of what batteries, well there isn't much choice tbh. I just run normal Duracell D cells. Alkaline isn't great, but it's an affordable option, they also offer huge capacity and long run times.
Options I can think of:
-AA converters. I believe you can buy some D sized plastic cells that allow you to fit two AA batteries in. This means you could run your 3d Mag on 6 AA's, either Lithium primaries, or rechargeable eneloops. The light should perform the same in terms of brightness as running on the D cells, it might even offer up a more consistent brightness due to the chemistry of the non alkaline cells. NiMH eneloops and Lithium primaries have a far more stable voltage level.
The main down side I suspect would be run time. An AA battery normally has 2000-2500 mAH, whereas a D-cell alkaline is around 12,000 mAH. I don't know for certain, but I'd expect the D cells to last longer - maybe someone could correct me if wrong though.
-Rechargeable D cells. Unlike AA and AAA cells, rechargeable D cells are not so common. What you'd ideally want is a Low Self Discharge NiMH cell, as these hold their charge well when stored (e.g. left in a torch) unlike regular NiMH cells which will self discharge quickly when left (1 week or so).
The trouble is, Low Self Discharge D cells are very pricey and you'll also need a charger capable of charging them. Also be careful, some rechargeable D cells, aren't really D cells. They are an AA or C cell in a bigger casing, so will have a lower mAH rating.
In terms of performance though, the Mag's have quite good throw and a good hot spot, so despite their low lumen rating, they are fairly handy. The smooth reflector gives them the long through, although it does produce a less than perfect beam with plenty of artifacts.
A glass lens will do two main things, 1. it will allow more light thru it, although if I'm honest I doubt the human eye could really tell the difference. I couldn't on either of my Mags where I've changed them to glass lenses. And 2. is far less likely to be scratched, the plastic ones can damage easily and become scuffed and marked.
The only downside to glass, is it is more likely to break if you drop the torch, but they are cheap enough to replace that I wouldn't worry to much.