The single best thing you bring up is your use of uplinks. In an ideal situation they should always control the flow of a battle and that is still your role, even in a squad.

I've found that I don't work well in a squad where everyone acts as assaults. You really can't support a squad acting like that. You can be the eyes of a squad (scout) using an eWar fit or with biotics. If you scout with biotics then you need to be able to run from an engagement. Quickly. Even more important to choose your battles in that situation. Maybe try and lead a group of reds into your buddies arms. Find choke points and ambush spots and use them to your advantage.

If you are looking for kills as a scout, often lone wolfing it is the only choice you can make. Point defense is also a decent strategy. If people are coming for you then they typically get closer than is comfortable for them. As in, within shotgun range. It's hard to be friendly with a swarm of super heated plasma pellets.

Some of my best games were spent running between blue controlled objectives and ambushing small groups after they thought they'd cleared the area. Cheap tactics? Absolutely. Unfair? Perhaps. Effective? Completely. Why should you play by your enemies rules?

If you're not using a scout's speed or eWAR advantages, then stop using a scout. Odds are another class would suit your playstyle better. Like someone said earlier in the thread, an assault shotgun is almost always superior to a scout shotgun in a head to head battle. That's why you don't go head-to-head.