Actually he IS that into you, it's just that . . .
Because somewhere in the email is something like this: "I don't think I can sell it."
What you, aspiring writer, are forgetting, is that while an agent may sell (as an example) mysteries and yours is a stellar one, he/she may know that his/her editorial contacts will not go for your particular mystery for some offhand reason. Agents, to varying degrees, sell to the same editors over and over. Examples: Jenny Bent (Trident) sells regularly to Denise Roy (S&S), Dorian Karchmar (William Morris) sells regularly to Claire Wachtel (William Morrow), Elaine Koster sells regularly to Carrie Feron (William Morrow), and so forth. The point is these agents know what these editors want . . . specifically. So if your novel's protagonist happens to be a coke addict and Agent A's contacts aren't much for characters with substance abuse issues, you're out of luck, no matter how deftly written your novel may be.
As always, everything in this industry is a crap shoot. Being at the right place at the right time with the right story. If you happen to have written a great book in the "vein of the Da Vinci Code" . . . well, I wish you the best; that train has already left the station.
Just remember, write the best stuff you can, the stuff that moves you personally. And never take any rejection (or acceptance, for that matter) personally.
And if you've written a great novel that just isn't selling? Well, that's why I'm here.
On topic, if you do not regularly visit Agent Kristin Nelson's blog (then welcome to the planet), you should visit it now. She has been posting query letters that turned into agency representation and deals. You can't pay for that kind of insider knowledge.