Maid has it right.
The first dungeon (or so) in a drpg (and related genre, often) is to get used to the mechanics of the game. It'll teach the basic battle system, make sure you know about any mechanics key to the game (maybe blocking, or elemental damage, or ways to stun, etc) and basically warm you up.
But at some some point, there has to be a 'gate'. The gate is not there to make sure you understand the basic game mechanics, but rather, to make sure you're actually using them -- that is, that you're playing right -- that you're exploiting weaknesses, that you're using buffs/debuffs, that you understand the game.
This is important. The designers don't want you to just level grind warriors up so you can attack/attack/attack your way through the game. A gateway boss forces you to put all the pieces together, so to speak -- for example, "oh, that's right, the game showed me how to go find better weapons... I guess I need to go do that now". They need to throw something difficult at you to force you to use the advanced techniques the game allows to avoid people skipping over important mechanics and playing 'badly'.
Probably the most infamous example of this is the Matador in SMT Nocturne. You could maybe grind for a couple dozen hours to beat him... or you could learn the press turn system and use it to your advantage.
Mars is 'that' boss. Hard enough to force you to really get to know the game mechanics. Part of the reason the game seems 'easier' after Mars is that you now have Mars at your side, but a greater part of it is that Mars forced everyone to 'get good' - proper battle tactics, learning how to find better weapons, etc.
Basically, a gateway boss like Mars is actually good design; you want to ensure your players truly understand the game's mechanics else they'll be frustrated the entire game, not just when sorting out how to kill one particularly hard boss. Plus it's fun to finally take them down.