Well firstly, Altis was introduced in 2005 May, so there is no "2004" Altis.
Now what you know is incorrect! Altis (both transmissions) actually runs better on CNG than a Prosmatec Civic, although both are fine, Altis is much better in this regard.
And Civic got the new eagle eye headlamps in 2004 (mid I think), not 2005.
Altis has the better resale, but Ive seen that the A/T resale isnt as good, which is vice versa for Civics.
Now, the pros and cons:
Civic Vti
Pros: Great stability and handling, excellent braking, beautiful engine roar, wonderful A/C, sporty suspension, refined quality and very fun to drive.
Cons: Stiff suspension, worse resale (slightly), sometimes underpowered engine, weak on CNG, no airbags.
Corolla Altis
Pros: Mighty engine, trouble-free car, soft seats, nice resale, cheap maintenance, 1 airbag and spectacular on CNG.
Cons: Dangerous braking mechanism (even with ABS/BA), poor A/C, very very dull car. Also, I have one and its key broke in less than a year, and that has been a BIG problem. Toyota Altis' key is (N) but the Civics is (Y)
Good luck, and any other questions, please ask.
Regards