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Okay, let's begin with what makes the two similar:

Both have high Special Attack
Both have high Special Defense
Both can function as team support
Both can act as the main Special Attacker
Both have Poor Defense
Both have poor Attack
Both have a decent amount of HP


And now for what makes them different:

Jolteon has access to Thunderbolt
Espeon Has access to Calm Mind
Jolteon has base 130 Speed
Espeon has Synchronize
Jolteon has Volt Absorb

Jolteon is the better pokemon in terms of stat distribution; its high speed allows it to annihilate opponents early and easily, or cripple them with Thunder Wave to help a Team-mate set up. It also has a far better attack option in Thunderbolt or Thunder in comparison to Espeon.

Espeon is outclassed by a few noteworthy psychic types, most prominently by Alakazam, who has a better stat distribution AND movepool. Girafarig is a better Baton Passer due to move selection and its immunity to the somewhat common Shadow Ball.

Jolteon is only outclassed by Raikou, and even then there are some things that Jolteon can do that Raikou simply can't.

It all comes down to what you want and what you like. I use both on my platinum team personally; Espeon acts as a good support for Jolteon and Jolteon acts as a mix between support and attack, helping the whole team out.

I picked Espeon and, honestly, my reasons are a lot less based on how they work in a team, rather individually (Also because Espeon is probably my favourite Pokemon anyway).

I still really like Jolteon, I find it's fast enough and has enough special attack to be able to support itself well (Especially when you take into consideration the fact that now it can learn Charge Beam which will boost its sp. attack more often than not) but there's something about Espeon that I feel is just that little bit better.

At the end of the day it just depends on what you want to go for. The two highest stats for both of them are speed and special attack, so it depends what you value more. I personally would rather go for something with more power behind it at the expense of being slightly slower (Although Espeon is still pretty fast) but like I said, it depends.

The main thing that annoys me about Jolteon (Now that Gen 5 is out) is its lack of Electro Ball, which would just annihilate everything. But that's a very petty gripe.

Either way, they're both good choices for their own reasons and I certainly wouldn't overlook either of them when I'm building type-based teams.