You take the hundred on the right, you take the hundred on the left, and I'll take the hundred in the middle!

Yea I had the same thing happen with my brother. He's a commando and I'm a Vanguard. He was able to deploy 3 when I could deploy 2. He was higher in level then me but I was further along in our story line. It seemed like the number increased for me in the middle of my level at the time. I think 25 or so. I want to suggest maybe it has to do with what level your crew skills are but I didn't observe his or mine at the time.

Things I've read and discovered that may help you. Affection does reduce time. Check the times of the missions after you pick them. That's when the affection reduction goes into effect. Otherwise it'll read the same on the list for all companions. Another thing: It may be tough now that you only have 2 companions. Your combat companion and your ship robot. Once you start getting more companions and higher level, not only will you be able to send them instead of the companion you're questing with, you'll also be able to send more then 1. Up to 5 at a time at 50 if what I read is correct. I haven't experienced a connection with how many missions you do to how long your next mission will take. The prefixes (IE abundant, bountiful, rich, etc) is mainly what effects the amount of time within a group level of missions. The higher the quality, the higher the time. It's fairly easy to out-level yourself with your mission levels. They are there to help guide you to know what missions help make up what level of equipment you can make. So even though you can do 33-40 missions, you may still need to collect mats from the tier before that to keep leveling your tradeskill.

A little off topic. http://www.swtor-spy.com/companions/ Look up your companion. If you get a gift they won't be interested in, save it for a companion that will enjoy it.