Muv-Luv Alternative is the highest-rated visual novel in VNDB. It may be worth reading at some point, but there's many huge flaws that in my opinion keep it from being truly great.

• Horribad pacing. It's often said that to fully enjoy Alternative, you have to first complete Muv-Luv Extra and Muv-Luv Unlimited. This takes dozens of hours, and for what? Some blink-and-you'll-miss-it foreshadowing amidst all the filler and becoming more "emotionally attached" when Extra becomes relevant in Alternative. Even then, Alternative doesn't become interesting until about a third or halfway through (that's maybe 15 hours), because it repeats most of Unlimited. I don't know how long it took me to finish the whole trilogy, but it could easily have been 50+ hours. There's other VNs with comparable length such as Umineko and YU-NO, but those actually have much better pacing as there is less filler and repetition and they have more unique content.
• Unrealistic/Shallow characters. Yes, the premise is to put these silly joke characters into a nightmarish war story, but come on. Most of them can be described with a sentence or two. Miki is a moe girl with a cat theme, and Mikoto's main personality trait is that she's "bad at listening at conversations", which she apparently inherited from her father in a bad case of Shared Family Quirks. The only ones to have any real depth/development are Takeru himself, Yuuko and Meiya Mitsurugi. And even in the case of Meiya I often got the feeling that when she expressed her political views, the author was talking through her.
• Shallow premise. Aliens attack Earth and Takeru has to save the world. The only aspects that make it stand out are the super exaggerated emotional elements and some examination of how humans would exist in such a dystopian world. But even the political elements are outdone in complexity in actual literature. (It must be noted though that the fan translation I read has been criticised and may have botched the intricacies of the plot, and the upcoming Steam version is supposedly better.) The melodrama also becomes tiresome after the 9586th instance of the authors pulling off yet another Diabolus Ex Machina or a character delivering a 10-minute motivational speech before heroically dying.
• Miscellaneous writing problems, such as the protagonist needlessly repeating and explaining in his internal monologue scenes that the audience just saw. The exposition is very poorly integrated to the story, resulting in hour-long literal lessons on the fictional society and aliens. And other problems that I've forgotten since reading this a few years ago.

There's other, better visual novels, which have superior pacing, characters, plot (due to being more based on the characters' choices) and so on. Here's some I recommend instead:

• Umineko (although I haven't read episodes 5-8 yet)
• Steins;Gate
• YU-NO
• Katawa Shoujo
• 999

YU-NO and Steins;Gate especially are great if you're into plot twists and melodrama.