Guilmon levels up faster. Agumon is one of the slowest when it comes to leveling up. Both get quite good Digivolutions easily. I'd usually pick Guilmon over Agumon, but I suggest you make your picks based on personal preference. There are no big disadvantages to either Digimon.
Agumon is more of a tank, able to dish out damage while also taking a beating. Additionally, he has excellent availability: He comes in what is arguably the best pack, and if you don't take it then he is still able to be recruited almost immediately after entering south sector assuming your team is powerful enough. He has early access to BlackWarGreymon, potentially getting him in his early 30s, if that! His only, and I mean ONLY downfall is his low speed, in both the stat and leveling. However, if you take the effort to get Agumon going, nothing will be able to stop him, especially once he has ninja-like speed.
Guilmon, on the other hand, fits the Berserker stereotype in my head: Kill them quick or be annihilated. Guilmon's DRI agent is available not long after Agumon's, since you have to complete the Sepikmon sidequest to get to WarGrowlmon. However, his pack is easily the weakest of the three, as Kumamon is not really enough to make up for having HealBotmon on your team, especially given that Kumamon is a huge exp sink that will more than likely leave all three underleveled, especially combined with Hotdogmon's slow leveling. As far as digivolutions go, Guilmon's best bet is the Metal Digimon line (MetalMamemon>MetalGarurumon>MegaGargomon) which fortunately helps his mediocre armor. Guilmon has a few more downfalls than Agumon, aside from those mentioned here are his low base stats. However, he has a surprisingly good Digivolution tree, with relatively easy access to Phoenixmon if you want a healer than can still dish out damage.
Guilmon manages to surpass Agumon a little after 40, as Agumon most likely will have to work toward Diaboromon while Guilmon can work toward Beelzemon, a much quicker process. This, combined with his faster leveling result in the following judgments.
Agumon is superior if you're new to the game, but a properly raised Guilmon WILL surpass him later on.
Call me Zurr. [They're called] something like "Snowy Fortitude" and "Speed of Jesus" - ZoneAlarm on LoL holiday runes