Your own assumptions are the source of most of the "bad". Why do you assume the alien from the fist film has evolved from this one? Both ships were thousands of years old when the humans encountered them, so the "alien" in the first film could be an older, outdated, bio-weapon; and just like you can find pictures of B-17s in an USAF office somewhere, they decorated their wall...
Cowards become heroes and vice versa all the time in both real life and other movies.
What sudden change in attitude to humans? When did thousands of years become sudden? The reason might be revealed in the next film... However, why must everything be explained? I like a movie I can chew on. If you watch the DVD/Bluray with the directors commentary, you'll realize that even Scott himself don't know if the planet where the Engineer sacrifices himself in the opening scene is Earth or not. It is deliberately left as a mystery.
ok, i'll bite this time. If you are implying the xenomorph from the original film is an earlier incarnation, then why didnt the engineers simply locate the crashed ship using the beacon the Nostromo located, and finish the job?
someone who runs from a 2000 year old headless corpse then suddenly finds a wormlike creature that is crawling through slime and thinks its adorable?? yeah right, totally believable.
wether the change in attitude from the engineers was sudden or gradual, no explanation or hint is given. To me at least, its just bad storytelling.
Its not an unwatchable film by any means, i'm sure I will watch it a few more times. It would have worked better as a standalone film, change the ship and xenomorph stuff, remove wayland etc and start a new film series