Most of those things you can say the same for the spindash in classic games.
No you can't. The spindash doesn't let you bash through any enemy with ease. Some have countermeasures for that reason. Level design also doesn't allow that to happen. Spindashing has other downsides that keeps it from being spammed.
Will you elaborate on how you consider these to be flaws, or how they are different from the Genesis Sonic games?
In the older games, automation, or spectacle whatever, was used sparingly. Usually it was after you accomplished a challenged thrown at you from the stage or its the introduction to a level and so on. Unleashed/Generations (never played Colors completely) always faced this problem where the whole stage was a grind/corridor fest and relied too much on speed instead of actual platforming. Where there was some platforming going on, it was in the form of floating platforms over pits or simple jump here and stomp there and homing attack to a spring.
Sonic's handling in Genesis games was always tight. You felt like you had control over him at all times and any slip ups were your fault. That isn't the case in the newer games where you can make a turn without drifting or dodge an obstacle without sidestepping. The second you don't do what the game wants you to do, you are punished. Hell, its hard to traverse through floating platforms without using the stomp to keep Sonic from falling off.
I don't even think you need an explanation on enemies. Sonic 2's Metropolis Zone should tell you how deadly enemies can be in the Genesis games and how they weren't merely homing attack chains for Sonic to cross a bottomless pit. It has become a running joke in some places about the design choice about floating enemies placed in a line for Sonic to homing attack.
Bottomless pits should go without saying. They are in every stage in Unleashed and Generations, they are only there to provide some kind of difficulty since the main hazards are pretty much thrown out because of boosting or half the level being played for you. They are only there for unforgiving deaths where you press Square instead of Triangle and end up missing a QTE in Unleashed and Generations uses them for any errors you make. Its just cheap and lazy. Why not just design stages that actually challenges a player's expertise or enemies that are actually a threat to Sonic? Older games only used them where it made sense like Flying Battery Zone. Most stages at ground level avoided the use pits and stuck to various amount of enemies trying to kill you, traps, or even puzzles*.
That's my elaboration in a nutshell, but I could have went on longer if I wanted to.
*Mostly referring to stages outside of GHZ and the like.
Already addressed most of what you said in my tldr, but there was this:
Because that's how you defeat enemies along with basic jump, slide. Also, any alternative that would NOT break momentum?
That's total bs. Homing attacks
do break momentum.
That doesn't really counter what I said anyway. Of course that is how you defeat them, but they are still there just to keep your boost meter filled.