Well, for both Pokemon you can breed with the wonderful Ditto.
Ditto can be found in the Desert Underpass in Emerald, so you can simply trade back. Or, it can be found in FireRed and LeafGreen. You can put Ditto and a Treecko/Grovyle/Sceptile/Mudkip/Marshtomp/Swampert in the daycare to get the Pokemon of that species.
If you can't get Ditto, then I'm sorry but this will be pretty hard.
You will need a female Treecko/Grovyle/Sceptile in Ruby and female Mudkip/Marshtomp/Swampert in Sapphire. (Of course, you can trade back and forth to get the Pokemon).
This will be very hard since it's very hard to get a female starter. (1 in 8 chance)
If you have got your female starter, you will need a male Pokemon that can breed with any Pokemon on the respected lists.
Any Pokemon here can breed with your Treecko/Grovyle/Sceptile.
Any Pokemon here can breed with Mudkip/Marshtomp/Swampert.
Any Pokemon here can breed with both.
^^ These Pokemon have to be male.
Now, you can breed your Pokemon to get your Treecko and Mudkip.
Sorry about this rather confusing answer. xD
Hope I helped. :)