I’ve got a 21′ aluminum pontoon boat. I can directly speak to your situation! 
So… as for towing, they’re a b**ch unless you have a decently beefy truck, preferably with a towing package. They are wider than your truck, so your mirrors will be occluded and, at 21′ plus a good 6′ of trailer in front of the boat, they are *long*. So they’re not easy to tow… that said, they’re not the end of the world to tow either. I used to pull a 20′ car trailer for work and it’s really a lot the same.
You will feel every bump and jostle, and sometimes the weight will want to push your truck around a bit. One of the scary spots is westbound I94, far left lane, entering the Lowry Tunnel. The trailer wants to keep going straight while the truck is trying to steer around the corner into the tunnel. You have to know what you’re doing a bit or the trailer’s momentum will push the back end of the truck sideways.
Also, my trailer only has one axle and I don’t care for that… plan on adding one if your trailer only has one.
As for how they trailer, I can’t speak to bunks, just scissors (my trailer is a scissor trailer). But I can put in/out on a beach, on an incredibly shallow launch, etc. There are some distinct advantages to a scissor trailer… you can beach the boat and then back the trailer under it, which makes things a lot easier. I can line the boat up with the trailer very nicely and get it centered, then lift it out of the water and pull it up on shore to strap everything down. I would say with practice there’s not a lot more time involved than loading any other 20′ boat, it’s just different.
I’ve never tried anchoring across the current… I usually only drop the bow anchor, let the boat swing into the current, then strop the stern anchor to hold it where I want it. Because the logs are long and skinny there’s much less drag on the anchor than with a regular hull. However, having to run back and forth from the console to the bow back to the console while you’re in current is a pain and at times downright dangerous, so I went for an electric anchor winch with a remote that I bolted right to the side of the console.
Regarding anchoring across the current, pontoon boats have so much space on the sides and ends that it’s really not necessary. You can fish people off both sides and the bow and stern at the same time, so no matter where you end up anchoring people will have room to fish.
I also cannot state strongly enough how important an electric tilt/trim on the motor can be… for launching, trailering, and river navigation, having the ability to get your lower unit up out of danger without having to leave the console is HUGE. This is the voice of experience talking here. Rocks and props don’t get along well, and having to leave the con while you’re navigating in current is never a good thing.
I wouldn’t go less than 20′ if you want any room to be able to fish unless you’re never going to have more than 3 people in the boat. Mine is 21′ and I’ve had 4 people in there with no issue. I could easily fish as many as 6 out of the boat with no huge issue provided that it was anchored in a good spot for people to fish off both sides. I snagged a couple chairs from an old patio set that I keep on the boat and I have some nice folding camp chairs that I use as well. That makes it possible to arrange the seating as best fits the fishing conditions and passengers.
If you’re going with a pontoon boat with no seating, though, storage is an issue, I ended up getting a 3’x2’x2′ heavy duty storage box that I bolted to the deck using u-bolts. I’m not happy with this arrangement though because it takes up the whole corner of the boat and people like to put stuff on top of it which makes it hard to get into. It’s always going to be an issue on a boat like this unless you have some under-deck storage, which is what I’d REALLY like to do.
I have Folbe rod holders mounted to the rails, 5 positions around the boat (2 on each side and one center astern) and that works really well for both trolling and catting. With a setup like that you can use planer boards and everything. Also since pontoons only have about a 6″ draft on floats that are a good 4′ apart, they are very stable and can get to areas where a regular boat has issues going.
One big thing of note: power plants. When I bought the boat it had a 35HP Evinrude on it and that was just not sufficient. I could get up to about 12mph on the GPS, and that was about it. So last year I upgraded to a 1985 90HP Johnson with a fresh rebuild from Robbinsdale Marine. I can now do 25mph and I feel much safer being on the river and needing to get back to the landing fast. Also with that much juice I can use the pontoon for fun times and pull tubes and stuff.
It’s been expensive… between the boat and trailer, new motor, electronics, batteries, gear box, rod holders, and so on I’ve probably got about $9k into it. I need to put new tires on the existing axle and I really want to put a second axle under it. So don’t plan on this being a cheap deal… if you get a new boat it’s going to be primo dollars and if you get a used one there’s going to be maintenance and upgrades and stuff.
All in all, I would say that for a platform for any kind of fishing, awesome cat fishing, and good general family boating fun, you simply cannot beat a pontoon boat, but there are drawbacks that you at the very least need to be aware of.
That’s probably way more than you wanted to know, but hell… I’ve had this thing for 3 or 4 years now and nobody here really seemed to have much, if any, experience catting the rivers out of a pontoon boat when I got it, so hopefully this post can be useful to yourself and others. 
