I think the best martial arts to learn is what you learn on the street. Karate, tae qwan do, ninjitsu all involve rules.
The idea is valid, but I would disagree with the inclusion of ninjutsu in that list. I did MMA for about 12 years, and had a brief couple month fling with bujinkan ninjutsu. It heavily favored doing what works over what's "traditional" or "fair" and even things like "smash their head into this conveniently nearby wall" and "why not pick up the chair and club them over the head with it" were pretty regularly part of the training.
"Rules" taught by specific martial arts and specific schools is a very real problem. Most karate and tae kwon do schools have their students train barefooted, even though very few of us go barefooted in daily life. Many schools use soft mats, even though there's more carpet and concrete everywhere else. When I did kickboxing and muay tai, most of the training was either done on a bag, standing stationary, or with a partner in a tiny ring. Bag drills are great, but fighting in a ring is very different than fighting anywhere else.
From your list, karate styles are probably the worst. (I did shotokan for 3 years and shito-ryu for 2.) You train barefooted and generally on mats (though to be fair genuine tatami aren't exactly soft.) Grappling practices (not native to karate, but everyone teaches it) tend to involve a lot lapel manipulation, even though nobody in real life wears gi tops. Fighting practice is often in regimented back-and-froth drills. Ground fighting is barely touched upon, if at all. There's a lot of focus on kata. Sparring contact is generally minimal. Very little of the material is applicable to fighting, and you might have to work through a year of learning bad habits before they ever get around to letting you try to apply them. Ippon kumite and related drills are good for learning control, but they're counterproductive for learning to fight.
Worse than karate though, would be aikido (I did aikido for six months) for one very simple reason: the uke/shite relationship. Basically, with aikido, you specifically train with opponents who are trying very hard to cooperate with you, and you are trained to cooperate with your attacker. It's a deliberate philosophical choice, and yes...it's true and a very common premise in a many styles than cooperating with an attack is an effective way to avoid injury (bend like a reed in the wind, and so forth.) But the way it seems to be taught in aikido (general qualifier: my six months at one specific school might not be representative of the style as a whole) crosses into the ridiculous. Basically, a lot of it doesn't work unless your opponent is cooperating with you. And unfortunately my experience with aikidoka is that they don't realize that. I spent a lot of time in my aikido classes standing there passively waiting for my partner to try to do some technique on me, only to eventually be told that I needed to be more cooperative. When a "senior student" with 3 or more years of training can't take down the new guy...that's kind of a problem. And it's not like I was going out of my way to be a troublemaker. The problem seemed to be that if you train for years with people who know the technique you're using and are deliberately putting their body where it needs to be to make it easy for you to do it on them...that's just not conducive to learning how to put somebody in that position yourself.
Anyway, among the styles I've studied, ninjutsu was probably the least limited by rules. Yes, we wore training outfits not representative of daily clothing. But we also trained outdoors, we trained in tiny cramped indoor spaces, we made use of the environment, fatal and debilitating attacks like eye gouges and throat crushing and other "unconventional" things that would generally not be taught in a more "sport" oriented style were all part of the curriculum from day one.