This is all really hard since it kinda sounds like you haven't even worked out your plot yet.
Are you more of a plot-driven writer?
Action-driven?
Character-driven?
Emotion-driven?
Theme driven?
It seems to me that aliens looking like us or not looking like us is a HUGE question to be hemming and hawing over.
What's THE single most important aspect of the story for you? After you've answered that question, make the appearance of the aliens service that that one key driver.
This is so spot on it bears repeating.
I feel that unless you have a well thought out world and plot line, you are begging for trouble when it comes to plot holes and characterization.
One of the biggest problems many writers face or mistakes they commit is coming up with 'cool' concepts that lack any real substance.
For instance, imagine reading a story where a character has the ability to create water. He can point his finger and it is like a fire hose, galloons and galloons of it gushes out. Now imagine this same character is stuck in a desert and dies of thirst while trying to walk to the neighboring village.
As the reader of this story the first question out of your mouth will be "Why in the hell didn't he make water for himself?"
This is a plot hole. A big one.
the problem with making stories with cool characters and concepts without well thought out worldbuilding and plot lines is that you are bound to make a bunch of giant plot holes that will piss the reader off.
I think if you are writing for YA, then you get some leeway because younger readers tend not to notice plotholes. But older readers do and SF readers probably moreso than others.
For instance, being the future, 25th century or whatever, wouldn't they have devices that would tell human from alien? Hell, in the 21st century we can determine your genetic disposition from a strand of hair. I'd think spoting aliens is no problem.
Anyways, just think through the story and world building and the answer should become obvious.
good luck
mel...