That's pretty much exactly why they did it. That, in addition to the self insert factor, various fanservice moments with the girls and the Love Hotel sequences are all reasons why the protagonist shift was Kaede ---> Shuichi instead of the other way around. It's hard to take the game's "anyone could die!" vibe at face value, when the odds were incredibly stacked against Kaede. I spoiled myself, but I probably would have figured out the twist in advance. Because if you think about it, Kaede doesn't at all feel like a traditional protagonist at all. She spends a good deal of chapter 1 being Shuichi's cheerleader and there are several instances where the player is divorced from her thoughts. If I'm being honest, Kaede left a bad taste in my mouth because of how cynical of a character she was (heh), even if her personality was kickass.
As an aside, I don't think "awkward shy male finds confidence because his waifu died" descriptor applies to Hajime (the God), and fits more with Komaru, who often goes overlooked.
If I had to rank the protagonist's I'd probably go:
Hajime > Shuichi > Kaede > Naegi's
For as much flack I give the game for Kaede's death, I really ended up liking Shuichi. To the point where I would have preferred if they hadn't bothered with the fakeout nonsense in the first place.