I think one of the problems with Togekiss is that it doesn't have enough moveslots to take out all of its weaknesses. Without Nasty Plot it doesn't hit hard enough to seriously threaten things like Blissey. Without Thunder Wave/Body Slam it isn't fast enough to flinch them to death. Without Subsitute it is crippled by status.
Not to mention trying to block status with a lum berry makes you prone to sandstorm damage/stealth rock without that boost from leftovers. If Gen 5 gave Togekiss 5 moveslots then it'd be fantastic, otherwise it is brought down by that one weakness.
Giving a pokemon like Togekiss a weakness or a counter adds depth to the game and if you ask me is sort of a good thing. If there was absolutely no way to counter a poke then it would be moved to UBER. Togekiss has its flaws, its special attack is high, but not enough to down a blissey without protection for Subs or Safegaurd. He is screwed if they can poison or paralyze him, but that is why there are pokemon with Heal Bell (like Togekiss :D) giving Togekiss Substitute is good for blocking blissey's toxics and T Waves.
Togekiss's other counter that is very common in todays metagame, Rotom-A, is not going to be an issue in Gen5 because he no longer resists/is immune to Togekiss's most common attacks, you will still need to worry about the likes of Zapdos and Jolteon, however.
One of the cool things about Togekiss is that he can do so much but only has room for 4 moves. You can go with Paraflinch or give him a 3rd attack, you can give him encore and mess up guys trying to set up on you, you can do three attacks and achieve better coverage. Zapdos, Rotom-classic, Rotom-S (lol flying+levitate) and that genie guy who is electric are the only guys who can resist Aura Sphere and Air Slash in gen5. Togekiss may have lost roost, but it also lost one of its biggest counters, a fair trade if you ask me.
If one is ballsy enough to forgo T-Wave and add a 3rd attack like me, then I would recommend something like this:
Item: Leftovers or Life Orb
EVspreads:
with Leftovers: 40hp/212SPAtk/252 speed (you will have 321 HP)
With Life Orb: 4hp/252 SpAtk/252SPeed
Timid Nature
Moves:
Nasty Plot
Air Slash
Aura Sphere/Fire Blast
HP Ice/Psycho Shock/HP ground/Fire Blast/Water Pulse(dat confusion)
HP Ice is for Zapdos, Rotom S and the genie. HP ground is for Jolteon, Electrivire, Metagross, and Heatran. Fire Blast is for Steels that are not named Heatran and tend to have 2nd types that resist Fighting. Psycho Shock can be a big F%$# YOU! to Blissey, but Aura Sphere is generally a better move. Water Pulse was a move I used on my first Togekiss at the start of Gen4, I like it, I like the 40% confuse chance, I was very surprised that it is never used on Togekiss (it kicked ass in Battle Tower :D).
Don't forget about Choice Scarf, Scarfekiss is an awesome revenge killer that is like a cool person's Jirachi with Iron Head.