I would say that what you describe is a MUCH better situation. If you have 100 small bills rolled into one, it's easier for representatives to say "I voted for this part, not that," or even, "I didn't see that part of the bill." With many smaller bills, it makes the tit-for-tat more explicit.
Representatives could still trade votes if they wanted, but we would have more visibility into the process. What's bad about that?
My thinking was that the time to pass a bill would still remain about the same, regardless of size. This means that we wouldn't see as many little bills passed as large bills.
I get your point about smaller bills providing better transparency. That's a very good side effect of smaller bills!
Not sure we'd see fewer bills passed; the cognitive load for each one would be smaller, so maybe they could work faster.
Anyway, "fewer bills passed" could be a good thing, depending on your perspective. The job of Congress isn't to pass as many bills as possible any more than the job of programmers is to write as many lines of code as possible. Less output may be better.
Representatives could still trade votes if they wanted, but we would have more visibility into the process. What's bad about that?