At this point, it seems like the only aspect of Megaman Starforce's game system I haven't talked about is the Mega Buster, Megaman's "main weapon" that is seen in every Megaman game. Of course, calling it his main weapon in the Battle Network/Starforce series is a bit flawed, since it is classically very weak in these games. The Mega Buster/X Buster/whatever may be extremely powerful in some Megaman (the X series comes to mind, where it tends to overshadow the boss weapons), but in Starforce it is little more than a weak side-arm that you only use when all of your Battle Cards run out. However, other that a few flaws, Starforce has the best version of the side-arm style Mega Buster that I have yet seen.
One thing that works well with the Megaman Starforce and Starforce 2 Mega Buster is that it is easier to control than in older Megaman games. The Mega Buster fires at full speed while you hold the button and charges while the button is released. It both plays to the basic assumption of using the Mega Buster (that you are charging whenever you are not shooting) without asking you to wear out your thumb holding the button down, and lets you shoot rapid-fire at full speed without forcing you to rapidly button mash. Because you don't need to hold down the button to charge, you don't need to be paying attention to your secondary weapon while using your primary weapon, the Battle Cards, and you can freely mix the two types of attacks with little effort. Other than the fact that it can be a little hard to tell whether you have a charged shot ready or not, the controls work beautifully.
Another new idea in the Starforce games is the ability to add on additional properties to the Mega Buster so it can do things other than raw damage. Megaman Starforce had several "Mega Weapons" (equipable parts that change the properties of the Mega Buster, essentially a simplified version of the more flexible Megaman Legends Buster Parts system) that add a negative status condition (like confusion, blindness, or gradual HP drain) to an enemy target. Thus, you could turn your Mega Buster into either a powerful attack weapon or a tool that let you disable enemies until you could activate more Battle Chips. Megaman Starforce 2 adds on to that even more, by adding new kinds Abilities that let you turn a Mega Buster shot into a spread weapon or use it to transform battlefield panels into Ice panels, Grass panels, or the like. With all of these properties, the Mega Buster is a versatile tool that can be modified in many different ways to become an important part of game strategies in a way it never has been before, at least in theory.
An overriding problem with the Starforce 2 Mega Buster is that its different modifications come from different subsystems of the game that don't interact and often contradict each other in unusual ways. The Mega Buster's basic damage capabilities and ability to inflict status comes from the equipped Mega Weapon, but spread capability and ability to transform panels comes from Link Power Abilities. Tribe On form greatly modifies the very nature of the Mega Buster charged shot, altering the basic statistics of the Mega Weapon and, much more problematically, completely overriding the ability to inflict status or equipped spread abilities. As such, while you are in Tribe On form (the default state for the latter half of the game), you can't take advantage of a lot of the Mega Buster's more strategic features, even if you are spending Link Power or giving up a lot of attack power in order to equip them.
One thing that could be done is to remove the entire Mega Weapon subsystem. It existed in Starforce to replace part of the Program subsystem from the Battle Network games, but since Link Power Abilities were designed to be a much more thorough replacement for that system in Starforce 2, Mega Weapons are no longer needed; everything they do can be folded into Link Power Abilities. Also, the modified Buster attacks of the various transformed forms should have been designed to be compatible with the spread modifications, and the fact that status conditions don't work with Mega Buster attacks is simply a mistake.