I've been playing Bowser Jr. (henceforth referred to as Ludwig in this post, because he's the best Koopaling and who I personally use as far as alternates go) quite a bit since I acquired the game. I've been doing quite well with him. 120 W/29 L so far with him. Not particularly spectacular, but I play in short bursts for a few hours a night, sometimes skipping a night.
Anyway, here's a few things I've noted while playing Ludwig in For Glory and against friends:
Regarding Mechakoopa:
1.) If the enemy is stalling, or keeping their distance, in many cases you can Down-B -> Double Jump -> Neutral-B. In a lot of cases I've noticed, most players either get hit by the Mechakoopa, jump into the Cannonball, or pick up the Mechakoopa and let the Cannonball fall onto them. Get a feeling for where the Cannonball drops compared to where you and the opponent is. It becomes second-nature after a while.
2.) The Mechakoopa has saved my bacon on more than one occasion. Having a Mechakoopa present on the battlefield at all times (or as often as it's safe), especially against powerful, projectile-happy characters like Samus and Megaman, is crucial.
3.) Mechakoopa makes for surprisingly good edgeguarding. This applies more for the characters that have strong vertical recovery specials like Ike, Marth, Mario and others. Chill near the edge double jump when they get close and drop a Mechakoopa on their face. It's not likely to kill them or even really gimp them, but free, safe damage is still free, safe damage.
4.) Don't underestimate the old adage 'Out of sight, out of mind.'. Release your Mechakoopa behind you before you attempt an approach. Most players forget about it because the camera zooms in and it disappears off-screen. I've used this to great effectiveness, including grabbing them and letting the Mechakoopa do extra damage before a throw, and having it save me from a failed read. If your opponent is too clever to just let Mechakoopa wander aimlessly around the battlefield, let it rebound off the edge of the stage and greet your opponent at random.
Regarding Kart Racin':
1.) Most of us here already know how to jump out of Ludwig's side-special. This is where the majority of Ludwig's mindgames comes from. If you're not using this special regularly, you're doin' it wrong. The point is to keep pressure on the enemy, keep them guessing what you're doing to do. Don't let the cart spin out unless you're trying for a KO. Always jump out of it otherwise.
2.) If you happen to hit the enemy while racin', they're usually popped up too low to hit with anything else.. except for down-air. You can get away with this up to 20% on some enemies. After that, you should be using neutral-air or up-air. If you're fancy, you can sometimes back-air if you jump out of the attack a little late.
3.) Speaking of back-air, if your opponent isn't good at grabbing you out of the cart or is shield happy, jumping out of the special after passing through them can sometimes allow you to back-air them when they drop their shield to punish. Alternately, practice jumping early and using d-air. It's considerably safer in most cases if you practice ensuring your d-air positions you behind the enemy to avoid being grabbed.
4.) If you have a roll-happy opponent, you can get free hits using this, especially at close range. Most of my hits with the cart come from chasing habitual rollers.
Regarding Cannonballs:
1.) The drop on the cannonball is, interestingly enough, one of Ludwig's best ranged tools. If you get good enough at it, you can use the drop to edgeguard. There's more practical ways to approach edgeguarding with Ludwig, but this is another possibility. Plus, it looks great when you pull it off.
2.) The Cannonball does surprising amounts of shield damage. In most cases, with some help with a Mechakoopa, you can get someone's shield down to a level where an f-smash will break the shield. Problem is, the window for this is so small, since shields tend to recharge fairly quickly.
Regarding Eject Button:
1.) When you use your recovery, it's good to note that as long as the copter exists, it's an active hitbox. This is especially useful when it comes to countering speedsters and rush-happy enemies, like Fox, Sonic, Little Mac and Captain Falcon. Many of these players tend to rush in to try to grab or hit you before you can do anything. Leave 'em a nasty little surprise from time to time, since if they run into it they're almost guaranteed to get an explosive present afterward.
2.) Ludwig's recovery move is easily one of the best and simplest edgeguarding tools I've had the pleasure of utilizing in a Smash game. Wait for them to approach the stage, drop the copter on their face. Easy. Even if they're not hit by the explosion, and are instead hit by just the copter's falling hitbox, sometimes the confusion alone is enough to net you an SD. This is more prominent when playing online, unfortunately.
3.) Ludwig's hammer attack post-ejection is a really strong KO attack. Unfortunately, it's also a risky maneuver to chase opponents like this, and is usually best used for surprises and chasing enemies with slow aerials. Learn the slight delay this attack has. You'll typically want to press the button just before you're lined up with the enemy to hit them. Alternatively, you can wait a moment to punish potential air dodgers.
Most of this advice has already been posted, I noticed, but I went ahead and posted some of it regardless. So, props to people that beat me to it. Hopefully some of this helps Ludwig (or other, unnamed pretenders) players.