I think the reason for Messi's speed is twofold;
1) To balance him out. Let's not forget which category he is higher in... I don't remember what the rating is exactly, but I'm fairly sure his quickness/agility, acceleration and dribble speed are some of the best in the game. If you max his top speed as well then he'd probably be even more ridiculous.
2) Anatomically, people with longer legs will have better top speed than those who have shorter ones, whereas the ones with shorter legs have better speed burst over short distance (acceleration). This is why I'm sure although Messi is a beast, I'm sure he'd be merely average in terms of something like... say... 100m/200m race. Not much he can do about that since it's just physical limitations. But of course, this does not matter much in football at all anyways. The other speed stats matter much more (agility, acceleration) and Messi has it where it counts.
My SO3 sequel fanfic: http://www.fanfiction.net/s/2678820/1/
My RPG hall of fame: SO2, SO3, FFIV,VII,IX,X, ToS, ToD2, ToV, Grandia 1/2
Well player ratings provided by KONAMI are usually awful, so you just have to wait ~2 weeks to get some new custom player stat database, much better than official one.
Can't say I agree with balancing in a football game; if a player is as amazing as Messi is in real-life, he should be head and shoulders above everyone else in-game.
His dribble speed is 98, but he's not exactly a slouch off-the-ball either!
Messi's stats are pretty good actually, he's not hugely fast compared to someone like Theo Wallcot, he's just better at choosing when to use it to get past people. The stats in Pro Ev are based on what a player is capable of, then a combination of their stamina, tenacity and form will effect his overall impact in the game.
To take Ibra for example, he has overall 97 due to having very high stats related to his position. But just because 97 seems high for what we see week in, week out at Barca doesn't mean they've f**ked up. When playing at the top of his game I don't think anyone will argue with the stats that put him at Ovr- 97(Att-95, Bal-96, DrAcc-95, ShPow-93, ShTq-98, Tq-97 and a fair smattering of other good scores + Trickster and various skillcards). The fact is Ibra has 72 for Tenacity so if his form is low or he's tired you can knock 10, 20 maybe more off when you combine the two if they're both bad. He may have 6 for form which is okay(maybe more based on his Inter days) and that might tempt you to field him in every game in your master league but that 78 for Stamina will quickly screw you if you play the way he likes to play(moving with the ball at his feet) game after game.
Its the intricacy of the stat system and how it directly effects every match you play that sets PES apart from FIFA IMO.
in terms of stats i normally use this guide when editing...
75 - 79 = average ability nothing special, anything less is considered not good at
80 - 84 = good ability, for example a player like fabregas' balance or shot acc
85 - 89 = very good, something they are well known for, lampard's shot acc or balance
90+ = world class, messi's speed, xavi's passing, drogba's strength, etc