Bedwyr: IMO, if you're looking to just do mounted combat, if you plan to stick to the rules (or the common rule extensions), or just have a casual one-off game with a friend, MegaMek is probably the way to go. If you're looking for something to do RPG stuff in, or want to play around with lots of other features, or if you're looking to run a campaign with multiple players, table top software is almost certainly the way to go.
Since I'm particularly fond of that method, that's what I'll cover, in case anyone else is interested.

My experience with MapTool has mostly been from the player front, with a brief dabble on the GM side of it, in both fantasy and sci-fi games, with both dismounted and mounted combat. For what it's worth, there are indeed paid software alternatives to MapTool, such as Kloogeworks. I'm just not a fan of asking my players to invest in software. Much better off asking them to invest in the game.

There are also other free alternatives, such as ScreenMonkey, but campaigns I've been involved with in the past that used it had mucho problems with it.
Personally, I like MapTool, even if there is a learning curve for the GM side of it. From the player's standpoint, it's relatively easy to use. And for the GM side, like any table-top software, you'll need to have a comfort level with making your own maps -- clearly it looks like you don't need help with that!

Things I like about MapTool (and table-top software in general):
- I'm free from confinement. I can bring on reinforcements, GM equipment failures, "bend the rules" by allowing players to use Edge and their CBT RPG gunnery/piloting skills in mounted combat, and use any map I want, from any source.
- Support for line of sight and lighting. Dear god, this solves so many arguments around the table, and it makes combat much more realistic without the pain of double blind rules. Clearly you've seen the advantages of that already
You could also use lighting to show an unit's ECM range. - Saving the game for later. Okay, MegaMek can do this too.
- Supporting multiple separate maps. The best case of how this is useful is when you're in a situation where your players are split up, like in a building or ship.
- Drawing and putting text on the map. Players LOVE this as a collaboration tool for planning assaults, and GMs love this because it's a quick way to show just how many player units just got nailed by that artillery shell.
- Users can create their own tokens. With a bit of coordination, everyone can create their own token from any image, like the photo of a mini or the character.
- Ability to color code tokens and indicate their status. This is great for visualizing which player has control over what units, or to show all the members of a particular lance, and the ability to mark enemies as down/incapacitated is nice as well.
Now that said, there ARE downsides to table top software. One of the big ones, of course, is that MegaMek at least handles the record keeping for you, which speeds things up significantly. I'm still trying to figure out a decent way to solve this problem beyond printing record sheets to PDF, in some way that the GM (or designated Master Tech) would be able to access unit stats to figure out repair needs and such. There might be a way to pull this off in MapTool, but I'm not 100% sure.
Another downtime is that beyond dice rolling, there's likely little to no support for the rules. I'll admit I've been glad to let MegaMek handle fire rules on the heavy forest maps before...
Finally, I can't say that the software is faultless -- I've seen some odd issues, from being unable to connect to maps not downloading.
To give you an idea of my recent experience with using MapTool from the GM perspective: At a gaming convention this summer, I had the opportunity to game with players from my old mercenary campaign that got cancelled due to relocation. And as much as I love my minis, I wanted something with a bit more flair and flexibility, something that would let me run with a BIG map and not need to take over 10 tables. And most importantly, I wanted to be able to save the battle if it wasn't finished, to wrap it up later (either at the next year's convention or a one-off visit.)
Well, I have a TV with VGA input, and a laptop capable of running an external monitor separately from the LCD display. And it's powerful enough to run 2 copies of MapTool -- one literally for the GM screen and the other for the players on the TV.
Now, I have Dunndjinni and it looks pretty, yet it and I do NOT get along well at all. Ever. Instead, I fired up Google Maps and spent about three hours stitching together images near Philadelphia, PA and labelling things to get this map, about 50x50 hexes:

That's at 25% of its full size (
http://www.not-quite.com/stuff/full-map-notation.jpg). I let the MapTool handle the gridding (not shown on these images) and just shifted the image around until I got as nice a fit as possible.
All told, I think I probably should have cut out about 50% of that map, but it just looked so awesome and tactically flexible from both attacker and defender point of view. And I was expecting to have to arbitrate quite a bit around the buildings, due to the tight spaces and half-hexes. (I wasn't expecting to have to mediate over whether a hex with a single tree in it would be considered light woods.

)
Again, this map was probably around 50x50 hexes -- you can probably stitch a smaler map much quicker, especially in non-urban areas and if you don't mind sacrificing some detail when you zoom way in.
(Ah, if only Google had a map of DefHes...)
Running this in place of a traditional table-top works, but you'll want a decent display and an extra USB mouse or two if you just want to use one system to manage everything and still allow the players to move things. Or have multiple systems and an ad hoc network. And it goes without saying that the real winner for this would be a projection system of some sort...
Or maybe the real winner is that I have the battle on this map saved safely for next year's convention.

Anyways, hope some of you found this useful.