I only got into Mass Effect recently (okay, a year ago) and I only beat ME3 for the first time three months ago (I went near-full paragon, synthesis ending, if that matters to anyone). I was not as disappointed as most (mainly because I knew what I was in for ahead of time), and actually liked the majority of the ending(s), but that part with the catalyst just pissed me off. So this is how I'd fix it:
1. Replace the Star-Kid (I refuse to call him the Catalyst, as I believe Shepard was the actual Catalyst) with Harbinger in hologram form (similar to the end of Arrival). Harbinger has already been established as the leader of the Reapers. We don't need to have a last second new reaper leader thrown in. Even if Harbinger said the exact same stuff as the Star-Kid (twisted logic and all) it would be better.
2. Don't let the player choose what the Crucible does. Instead, base what it does on the reputation bar. Full Paragon = Synthesis, Full Renegade = Control, Mixed Alignment = Destroy. War assets can still effect the severity of each ending. This way, every choice in the game matters.
Or we could go with my personal favorite...
3. Cut out the Star-Kid scene entirely. Instead, after Shepard defeats The Illusive Man, he walks over to the control panel and allows the crucible to dock. When it has, the control panel displays a new button, which Shepard dramatically presses. This begins the crucibles activation. Shepard sits down with Anderson (or alone, if Anderson died) and they have their scene. They both die next to each other, staring out at Earth. The crucible then fires (see point 2 for what it does) and the rest is the same.
Do you guys agree?