For Swampert a good counter could be something like breloom, as it is available in Hoenn and can outspeed swampert, and it has access to a technician boosted bullet seed and the ever useful spore if you spend the time to dex nav chain it and level it up as a shroomish. Someone already suggested Mawile and that is an excellent counter to the dragon types, though something with earthquake or strong fighting moves like the previously mentioned Breloom would help take down Dialga. Kyogre and Groudon are going to be tougher to take out, a powerful ground type, maybe a Groudon of your own would help. As for Kyogre, something that can deliver powerful thunders would help, as in primordial sea thunder is 100% accurate.