Halo:CE was a brilliant game of it's time, it is just considered low by today's standards.
I completely disagree with you about Halo's story though, as well as Bioshocks'.
Complaining that Halo's plot doesn't make sense is like complaining that The Transporter or Wanted aren't realistic enough. It's not supposed to be taken seriously. Master Chief is not meant to be anything more than the nameless, faceless badass in the suit, and you're not meant to feel any emotional attachment to him. The Covenant are not meant to be anything deeper than big mean aliens to kill or be killed by. It's basically just a premise to get the levels rolling, and should be judged as such, not as an interactive philosophy thesis.
Master Chief is meant to be seen as much more than that actually. He is the last hope of the human race who has been fighting a race more advanced than them for over 20 years. He is faceless because we are not supposed to sympathise with him as a person, but rather what he is. Kidnapped at the age of 6, brainwashed into following orders and never losing, forced through painful physical procedures and a man with all of humanities hope resting on his shoulders.
The Covenant resemble the Crusades, a religious group intent on wiping out all non-believers for the sake of reaching their promised land. They will stop at nothing to destroy all those that stand against them with no mercy shown.
Humanity has been fighting for over 20 years against a collective army which is years ahead of them in technology, they can never win a battle in space unless they outnumber them by at least three to one and even then they always sustain heavy losses, they have to sacrifice their ships including everyone on them to stop their enemy capturing them, or else the location of earth could be discovered.
They have to put all their faith into one man because the rest of the Spartans were all thought to be killed and so he is the only one with the ability to turn the tide of the war.
I'd say that has much more depth than a lot of other games stories, even Half Life's, the thing is that Half Life just portrays theirs a lot better and so people think it's actually got more depth.