Karthus's design is stupid and is the most poor-play-forgiving champion in League of Legends.

His passive lets him do a majority of his damage even when he gets caught and dies immediately. When he is dead, you cannot silence him, you cannot stun him, you cannot push him away, you cannot do anything other than get out of his defile and survive his ult. His kit makes it so that no matter how bad he did, he can always farm back up and pick up a few kills from finishing off people in teamfights and then proceed to carry because of his huge AOE potential and non-negligible ult damage.

Every champion has counters, but what is Karthus' counter. You have to focus him down or his AOE damage will melt you, but once you kill him, you still have to re-position and get out of his defile, and even then, he can still ult you. What the heck? Annie gets caught and dies before using any skills, GGWP. Cassiopeia gets caught and dies before using any skills, GGWP. Kennen gets caught and dies before using any skills, GGWP. But Karthus? Nope. He is the only champ who can still do a majority of his damage even when he gets caught.

And don't say build MR. MR will help against every AP champ, the fact that Karth will hit EVERYONE (Everyone needs MR) even when he's DEAD (Can't focus him down so he can't do any damage) doesn't make him any easier to counter with MR. In fact, he is probably least affected by MR.

By the tone of your post this prolly won't accomplish much but here we go.

1. You say his ult is negligible but despite what you say mr helps alot. That aside, a BV makes karth qq all day.
2. Karthus has no escape and no cc other than a meh slow that you have to walk through for it to work.
3. I'll give you that his passive at best makes you reposition and at worse picks up a kill or two but really he isn't the only champ to have a mechanic like this. (kog and zyra come to mind)

Not even to mention he is beaten in lane by most everyone.

Long story short, there are far more champs that need attention than Karthus

You ask how to counter him....Then say that mr counters every ap. figure it out buddy, its not that difficult.

I mean...tons of ap mids will counter Karthus in lane. Lux, Katarina and Ahri should all be eating Karthus alive, denying farm and fleeing from the defile once dead in lane. If your mid did a good job then Karthus' damage will be neglectful during team fights and even a basic Lux Barrier, Soul Shield or Black Shield will let you walk ult free.

False, Karthus's design doesn't reward poor play. It rewards consistent farming and good lane control. You have to actually be good at this game generally speaking in order to play Karthus.

A Karthus that doesn't farm can't just walk into a fight aggressively and expect to profit. He has to have damage to do that. He also has to time his entrance into the fight well and not get sniped.

Yeah, objectively speaking, Karthus's ultimate is his least useful ability. The most powerful parts of his kit are basically his passive, his Q, and his E. Everything else is extra.

Wait, you're complaining that you have to wait 7 seconds before re-engaging the team? Wait 'til you face even the neutered Tryndamere.

Everything about Karthus requires exacting play, and if you either fail to lead, fail to time, or fail to position (i.e. you have to get all three with exacting precision) you lose. My guess is you're a newer Xin Zhao player who picked him up because you thought Xin > all; that's what you sound like anyway. What probably happened is that you went up against a decent (or better) Karth, who knows that Karthus dies precisely when and where he means to (it's almost like he's a wizard or something).

How do you counter Karth? Step 1: remember his ult; look up the damage it does and remember to bank that much extra, with buffer. Step 2: remember his passive and learn to disengage and re-engage. Step 3: remember the WoP and get ready to juke it. Step 4: remember the Ping and learn to dodge. Kind of like most champions; you take steps to counter their abilities, often one at a time. If you're playing a champion that can't do any of these four things and still engage Karth (e.g. Xin Zhao) then respect the lich and don't feed him. If you're playing a champion that is specifically geared to doing these four things and still engage (e.g. Blitz), or who can ignore these four things and still engage (e.g. Gallio), then proceed to make the lich spit foul feeble and futile curses at you.