I think AC3 is my favourite in the series, tho I haven't played it in a long time and I just have the Japanese version, so I didn't "get" everything at first sight but still thoroughly enjoyed the game.
Anyways, for many fans the draw is exactly that: inhuman penalty for failure, forcing you to save the game before attempting any mission and repeat it with different AC, weapons and strategy. Once you grasp that aspect of the game you'll find the small features that re-balance the aforementioned "inhuman penalties", the most important one being the fact that you can sell your AC's parts at the exact same value that you bought them. This is pretty much the fuel to the "neverending tinkering-circle"(lol). This series surely is not for everyone, if you don't find enjoyment in 10-minute mission/30 minutes of tinkering - rinse & repeat till you get it right, then I'm afraid there's not much you can do in the game.
On the bright side, once you get the hang of it it's one of the most rewarding series out there IMHO. Just knowing that you actually beat an at first seemingly impossible mission with just a few chips of damage and even get a new part as a prize for S-Rank-ing it... good feeling
P.S. As a reminder, most energy-based weapons don't need ammunition = less expenses post-mission.