A few things worth noting in this campaign.
1) I am using the limited research admin option - based on nuclearslurpees house rule - and it works really well. You really appreciate the individual scientists, even the 2nd or 3rd best in each field, and a 20% 5 lab scientist is valuable. You also start to appreciate the 'lesser' techs, as you are researching far more techs simultaneously. While overall research is reduced to some extent (due to the greater use of lower % scientists), the 'main' techs, such as propulsion, proceed much more slowly, giving the campaign a more long-term feel.
2) Large hybrid carriers. I finally have got a good Battlestar Galactica campaign running and the most apparent impact vs a 'normal' campaign is how much you value the individual ships when you have so few of them. I started with six 'warship' Battlestars and four 'survey' Battlestars. That has now grown to ten and eight. When you only have ten major warships, you really care about each one, which adds to the overall roleplay of the campaign.
3) Squadrons. Managing large strikegroups is so much easier with the squadron options. I've been doing some tweaks in the UI, especially around detachment and movement orders, but it is really working well now.