LamoTheClown

I think if you're willing to put the effort into making the river treat certain classes differently then it would at least be really cool to try out. So long as you'd be willing to erase said effort if it turned out badly. 
 
P.S. You, sir, are awesome. I am so excited for this to be playable.

I've played this game a ridiculous (unhealthy) amount. And from what I can tell you seem to be off to a great start. I spend my time playing evenly between 5 or 6 classes and I think that 3 routes is enough. So here's my two cents:
 
Check out a modified version of ctf_2fort called ctf_2fort_saraya. It's the pinnacle of what a good ctf map should be (in my opinion). It allows for more variation a alternative routes. As in 2fort, make sure that not every route leads directly to the intel room. 2fort has three ways to enter into the fort, but only two ways to get to the intelligence. This allows for high variability in a player's attack options because theoretically, six different routes could be taken to get from your base to the enemy's intel. Its also great because the top entrance is only available to scouts, demomen, and soldiers. Any map with a top level like this where snipers are present need this kind of class-exclusive entrance. Koth_harvest has an entire roof available to snipers but the roof is easily accessed by certain other enemy classes. It also makes playing these three classes more relevant on offense.
 
Speaking of top levels, they're just plain awesome for the scout. Maps with multiple levels are way more fun than maps with only a few. Try maybe allowing roof access for scouts to jump around on. Or even just tall rocks. It would be even better if there were an entire route from base to base solely above ground level (a la 2fort).  Also if the snipers can see each other, its pretty epic (a la 2fort). This is my main complaint against koth_lakeside.
 
Here are some things to keep in mind when considering class balance:
 
Tight, winding, short corridors favor pyros and heavies. 
Paths which exit into wide open spaces favor snipers.
Rooms with one entrance/exit favor demoman and engineers.
Wide paths allow spies to easily get behind enemy lines.
Upper levels make it easier for scouts to get away.
Rocks and other obstacles in open spaces favor the medic (The medic needs something to hide behind while he heals other players, since he's most targeted class) and encourage clever engineering. You can see this in pl_badwater.
 
BUT IF YOU REMEMBER ONLY ONE THING, it's that options are key.
 
I you have a base with only one ground floor entrance make it two (like 2fort). If you have an intel room with only one entrance make it 2, etc. etc. even if the entrances are right next to each other and lead to he exact same place. This discourages camping. But of course there's a fine line between options and chaos.
 
I'd love to be able to test this out once you have it ready.