It's hard to make recommendations when you don't know what the game structure is going to be.
- Squad design.
The best squad design was the original - 3 teams with character switching and the tactical map for placing waypoints. The only things needing changing were improving the AI of the team, improving the pathfinding, and increasing the number of operatives. The squad order system was well implemented. The advantage of character switching was a more varied experience. The original game design allowed players to go anywhere on the map in different directions, and made the game more open ended in design.
It seems evident from game design that character switching is passe. nearly all games today are single character. Most games either have no squad control or only 1 squad and do not support waypoint setting. That has been replaced by line of sight commands.
This is much more limiting than the original design, you cannot send squads to far points of the map, your FOV is now limited to the area of the map you can see in front of you. That has led to more linear game design, with restricted maps and linear objectives, with more emphasis on scripted events which require tripping script triggers. If you liked the original game, these changes can hardly provide the same game experience.
However, if you are faced with a decision to make a single charcter, 1 squad game, it doesn't mean that the game has to be linear. If you want to make up for the absence of multiple squads, you have to make the single squad concept work - the team AI has to be very good, they have to be able to recognize their environment and use cover. Most important, you have to have very precise control over your squad. The best solution would be to be able to give orders to any member or combination. In other words, I could order 1 man to recon forward while ordering the other 2 to flank, while I flanked from another direction. You need easy to use, intuitive orders. The most important is a precise "go to" order to place team members exactly where you want them, coupled with the old ROE modes where they either attack any enemy or recon, attack only if attacked.
The context sensitive commands in GR 2 were very well implemented and should be looked at.
You need to be able to move your squad members around the map, be able to have them recon the enemy, be able to order them to attack, suppress, use stationary weapons, hold in place, defend a position, use AT, place charges. There should be a quick command to order them to go from defensive to offensive. If you could implement this kind of squad control, you will make the game far more tactical and increase replayability.