I wasn't happy with Full Metal Panic Sigma from the beginning - the art was worse than in the original manga and for the longest time frankly insufficient to capture the drama (e.g. in volume 5). More problematically, Sousuke experienced a completely implausible personality change after the first manga. In v4, for instance, he
makes the kind of demands he'd have considered 'terrorism' in the first manga. Bizarre.
The mecha battles are very hard to parse and exemplify the worst parts of shounen manga: The hero wins only because the hero wins because the hero wins. The last arc is an excellent example of this - suddenly, Sousuke can surpass any odds, no matter how overwhelming...
There are also way too many badly drawn (almost) naked girls, and girls in badly drawn bikini armor. These things are bad enough when they're drawn well, but when they're drawn badly, it's just...sad.
Then there are issues with characterization throughout the series, but I could maybe forgive those if the story itself were good.
Which finally brings me to the true issue I have with the story, the issue which makes me wish I had never read Sigma: The ending is ethically abhorrent and infantile. Spoilers follow.
"Black technology is not something that came from people a hundred years into the future. It is the product of a never ending eighteen year cycle that repeats itself endlessly."
The heroes are confronted with a Groundhog Day scenario, in which you have a moral duty to optimize. What that optimization looks like depends on the specifics of how time travel works. For instance, what happens to people in the original timeline if you change the past? Do they disappear? Is that like erasing a whole timeline full of people? Or do they just change?
But none of these issues is truly addressed. Instead, changing the past is bad mainly because it's the plan of the evil antagonists. So obviously, the 'right' choice is to forego the option of time travel. Dead people stay dead, Sousuke remains a murderer with a head count of >100 people etc., but as long as heroes are responsible for murders, it's apparently alright...
In fact, the choice is so bizarre that the author has to bend over backwards to make it appear sympathetic, by pulling a Kurz-isn't-really-dead scenario. So it's apparenly enough that Sousuke's closest friends are still alive, never mind Kalinin, or the dead whispered girl, or the millions of war victims...
You know an author has screwed up when the 'heroes' win and end up looking worse than the villains. But it's all fine because Sagara is "a nice kid" because he couldn't kill a 123rd person or something. Ridiculous. You want to be a truly nice kid? Then act like one by fixing your past.
Instead, making the bad choice is fine as long as you feel "I have to live with that burden [of the people who died or remain dead because of my choice] for the rest of my life"? Same with Kaname's thought that "This couldn't possibly be a mistake. Right, Sophia?". Well, if you are completely self-centered and don't have any compassion for your fellow human beings, then maybe. But I had (wrongly) assumed our protagonists were better than that. They get their personal happy end, sure, but at the cost of the happiness of the whole world.
A final Groundhog Day comparison: I felt as badly about this ending as I would have if Phil, the protagonist in Groundhog Day, had found a way of escaping the time loop without saving e.g. the guy who was suffocating. Even worse: What happens in Sigma is like Phil deciding he must make the 'tough choice' of not saving the guy - although he could.
In conclusion, the ending is horrendous and pathetic. If I'd known the series would end in such flawed Hollywood morality, I wouldn't have finished it. I wish I had never read Full Metal Panic Sigma - the first manga was pretty funny after all.