thought I would take a moment to answer your post.
I believe both of these models are fine amplifiers, I have heard the A90 (I find it to be a nice amplifier that covers most bases as far as I am concerned), also I have no experience of the A3.5. But I figure it must be a good amp based on Musical Fidelity's fine reputation for building good amps. (BTW I know the old A3.2 integrated (good amp IMHO), also I know the old A3.2CR pre/pwr amp (fantastic combination, just wow!!!).
So for me it really boils down to personal taste. If possible ask your dealer for a home demo, that would be the way to go.
Otherwise, since the Missions 780s are not huge speakers, you may want to take your speakers and CD player to the dealer for a A/B comparison of both amps.
Also the Arcam has well designed tone controls, and you can adjust the sensitivity of each input. So if this is important to you, the Arcam may just swiing the deal.
In any case, I am sure both amps are a safe bet with your CD player and speakers, and should lead to a nice well balanced system.