Why would you want Eli to be despicable? MGS has never truly had "Evil" villains, rather they've always been individuals who thought they were doing what was best. A true villain always sees them self as the hero. Liquid was only seeking to prevent the dying of the Genome Soldiers and fight back against The Patriots, his methods for doing so may have been wrong but his intentions were in the right place. Solidus too sought freedom from the Patriots and in MGS2 I never saw him as the bad guy at the end, in fact I really wished I didn't have to kill him as I agreed with everything he did, for the most part.
Eli/Liquid should explore how he came to be the way he is, how his experiences as a child and Big Boss shaped him into the person he would become.
Liquid: Can't you understand what its like to know that you are garbage from the day you were born. But, I'm the one father chose.
Solid: So that's why you are so obsessed with Big Boss, some warped kind of love?
Liquid: Love?!? It's hate! He always told me I was inferior and now I'll have my revenge. *laughter* You should understand me brother, you killed our father with your own hands. You stole my chance for revenge! Now I will finish the work further began. I will surpass him! I will destroy him!