Luckily (?) such thing as the ultimate Pokemon does not exist, even in ubers (although Ghost-ceus comes pretty clsoe to unbeatable in 1v1).
The outlines for this kind of discussion is probably a bit too loose to make points in. What is considered good? Is having the least amount of checks good, or rather it having centralizing effects? Doubles or Singles? Should we only judge single sets or consider the Pokemon as a whole?
Now, there aren't any non-Uber examples in Smogon because they usually strife to prevent overcentralization. Good (albeit Uber) examples of something being overcentralizing but nonetheless not being uncounterable are probably Xerneas and its predecessor Kyogre. Both of them dominate the Singles Uber metagame (Kyogre even leads the Uber Doubles - TopOgre anyone?), Xerneas being in almost 40% of all teams while Kyogre in the past generations even managed to break the 60% mark at times. However, both of them have in common that they can be countered, unlike some of the lesser powerhouses. Xerneas runs against a hard counter Aegislash and the wall of steel Mawile while Kyogre usually can't break Gastrodon and Ludicolo (and Shedinja of all things).
Don't get me wrong, even though it is possible to stop them they are considered the leader of the metagame for a reason; many people use them and many more have to be prepared to face and survive them. Come to think of, DPP Garchomp probably comes close to fill this role until it got the boot. It is not entirely unstoppable but works on the broken evasion mechanics which makes every encounter inherently luck-based, considering that sand was basically the only weather in OU and permanent.
The second kind of powerful comes in them not being counterable. A good standard example is probably BW MixMence (not DPP Salami becasue it got kicked to Ubers) or BW2 Hydreigon. The first one can smash its way through many walls with the two most powerful and almost unresisted moves in the game coming form both spectra while Hydreigon is able to tech its way through with its coverage moves (Blissey was a workable wall before it got Superpower in BW2).
However, both of them are relatively easy to check because at that time the metagame was revolving around base speed 108+ which leaves them rather easily checked and revengekilled.
The closest examples we can think of that fit both criteria are Mega-Gengar, Mega-Kangaskhan and Mega-Lucario to a lesser extent in the 6th gen Singles. Gengar is the most broken thing in the game as far as support is concerned thanks to Shadow Tag. Being immune to Toxic allows it to dispatch anything in the game that is not able to dish out enough damage and Perish Trap it while the nature of its ability allows the player to choose exactly which target dies. Its top speed makes it able to fire off Destiny Bond on anything that does not carry a Choice Scarf or rely on priority which, again, cannot be outplayed because of Shadow Tag. All in all, it basically always trade at least 1-1, just that the player dictates the conditions.
Mega-Kangaskhan and Mega-Lucario are powerful in a much simpler way. They are primarily sweeper, they just smash things and things die. Lucario gains enough speed to outrun any common Pokemon while Kangaskhan can allieviate her middling speed with the equivalent of a CB Sucker Punch. While they are pretty similar in function we think that Kangaskhan is more powerful because of the stronger coverage moves and the titanic bulk, even though Lucario has less counters and checks. Kangaskhan can only be countered by Gourgeist and Cofagrigus and only be checked by faster Fighting types resistant to Sucker Punch, namely Infernape, ponies and Mienshao. Except for Terrakion the subpar Cofagrigus everyone is easily checked by the omnipresent Talonflame, so that idea flew right out of the window (pun probably intended).
Lucario is much frailer and relies mostly on the STAB Adaptability moves to deal massive damage. Other than Kangaskhan Lucario cannot fit all its potential onto one single set but relies on the opponent making the guess which one it is running, similar to DPP Salamence, except that there is even less room for mistakes considering how powerful a Adaptability CC is. Still, we think it is a lesser Kangaskhan despite it being a Kangaskhan check.
So yeah, the best Pokemon is either Mega-Gengar or Mega-Kangaskhan.
Note, that it only applies to Singles. In Doubles Lucario is a bit too frail and is only able to target one opponent a turn and this kind of Gengar is limited to dedicated Trapper teams. Kangaskhan lacks the important Earthquake coverage because of the weakened power (and the sheer utility of Fake Out) but still is one of the most powerful Pokemon alongside with Charizard-Y.
Ironically, because both of them are the most dominant forces of VGC, Garchomp is the most used one despite being quite weak compared to them. Its main selling point is it being faster than both of them, Rough Skin against Kangaskhan and Rock Slide against Charizard.
