The issue is not that some upgrades have consequences that degrade some aspects of the weapon. As you point out this kind of trade off is good design that forces the player to think! The problem is that the negative aspects of most upgrades are SO strong that they actually make the weapon worse. It's not that they curb the weapons power a little, they actually make it hands down worse than if it hadn't received additional upgrades at all, while also wasting upgrade points.
As an example lets look at the Projectile Cannon (just the easiest example, if anyone is curious I am happy to produce math for other weapons). If I put three points into recharge time the weapon does 60 dps with decent accuracy and range. This is 30 damage / 0.5s = 60dps. If I then put a point into burst, the weapon fires two shots, each doing 30 damage, and has a rof of 1.5s. Now the weapon does 2x 30 damage / 1.5s = 40dps. Yes only 40dps, it also has worse range AND reduced accuracy. It is in NO way better after this upgrade. This doesn't create interesting choices for the player, it only creates frustration.
Hopefully this example is helpful. I don't mean to be rude about the weapon design. I just want to point out that tradeoffs are good, but choices that are undeniably wrong only hurt the game.
