I dont want to talk disadvantages of moding, but I try to explain why I think modding the game is not bad move. Becouse now I play modded version of AP (XRM - X Rebalance Mod) I will speak of my expirience with this mod.
1. In vanilla AP playing as Terran is very limited. XRM gives new possibilities such as full terran economy and more (more ships including TL, Terran (USC) Police License, HQ for player...)
2. Better weapons system - each race has its own (racialized) weapons and they are all balanced (except Mass Driver, IMO its overpowered now). So for example player will not be able to mount split weaponary on borons ships (i think its very resonable). Some ships have more turrets etc...
3. Ship extensions - like Jump Drive - are much more expansive. In vanilla AP player can afford JD very fast. In XRM AP we realy need to work hard to get one. And even if we have enough money JD ware size was changed to XL so small fighters are unable to have one aboard (IMO really good move)
4. Universe - AP universe map was redesigned (just a bit) and about 50 new sectors was add. New sectors fit really nice in oryginal AP universe, there are also some "shortcuts". With new background and sounds all that looks really good!
Universe is not safe! The danger is everywhere and player can't feel safe even in core sectors. Pirates are now dangerous, and we will not see pirates Zeus alone without an escort. Xenons fleet invading other races sectors are really fearsome. And more - Khaaks are back in the game. They got very good corvetes and destroyers. Khaak military transport ships are not easy prey - thay can launch numbers of fighters to protect them or attack other ships. Sectors controled by hostile races are not as empty as they were sometimes in vanilla. And lasertowers, orbital defence platforms are structures that are really a chalenge. In vanilla AP terran space was preaty safe, now xenons, khaak and pirates wont avoid them, if they find weeknes in terrans defences thay will try to take advantage of this situation.
Shipyards, Research stations... - all was rebuild, In "standard" shipyards we can buy only military ships and stations, all others was moved to corporations watchrooms. (personaly i like that idea) There are also corporations research stations, they have random location (mostly in unknown sectors) and can change their locations during the game. In that research stations player can buy advanced / prototype ships (and they are really good - but not overpowered).
Defences, configurations... - in pure AP lasertowers are like whisk

Military Inteligence Network with connection to Police Licenses that player have. This gives a huge advantage and much more possibilities... (check it yourselfs)
Above I give few reasons that in my opinion make modding worth.
Now few words to opponents of modding:
I fully agree to:
- Its EGOSOFT job to make game better;
- It would be better if we had no reason to mod the game
But:
Who know better than (WE) players how our favourite game should look like? Mods are made by players for players.
If we can make game better why not mod it?
The game in vanilla version is enough. Well at start I can agree, but in later-game its boring and XRM is at last trying to fix this.
But as I write at start there is as much fans as opponents of modding. I was not my intention to convincie anyone to mod his game. But I think idea of modding its worth consider, especially when Rebirth will not see daylight soon.