Been looking into the game in a bit more detail today. Since Alchemist is one of the most straightforward of the classes, it's the easiest to analyze. So as such, I'll go over the skills and how they relate to each other. I'll be using some of my own made-up translations for some of the more complicatedly named abilities, so bear with me. Hopefully you'll understand which abilities I'm talking about in the end anyways.

Stat Boosts/Escape Up:
They're the same for every class, so I won't even bother going over them just yet, except to say the following:
L10 HP Boost maxes at 145%. L10 TP Boost maxes at 192%. The boosts to the other stats are +1 per level. Escape Up maxes at L1.

Fire/Ice/Volt Up:
Max Level: 10. No Requirements.
Like all Mastery Skills in EO2 (with the exception of Medic's Healer), they begin at a 102% multiplier to their skills at L1, and climb by 1% per level, maxing at 111%. Not a lot, but at least it's something. Oh, and Alchemist Masteries are applying themselves to the full base damage this time, so they're actually useful in that respect.

Physics Up:
Max Level: 5. Reqs: L3 STR Boost.
Again begins at 102%, but has a max of 5, so you get 106% max boost out of this.

Analysis:
Max Level: 5. Reqs: L5 TP Boost, L5 TEC Boost.
When you're using a spell that targets an enemy's elemental weakness, the damage will be multiplied by an extra amount. Begins at a 105% multiplier at L1, maxes at 155% multiplier at L5.

Tier 1 Fire/Ice/Volt Spells:
Max Level: 10. Reqs: L1 Element Up of appropriate Element.
The base line spell. Single target, and TP Cost, Base Attack, Accuracy and Speed all rise with levels. Note that damage does not rise as a multiplier: it's more akin to having a stronger weapon. L10 Tier 1 costs 26 TP, 113 Attack, 195 Accuracy and 140 Speed.

Tier 2 Fire/Ice/Volt Spells:
Max Level: 10. Reqs: L5 Element Up of appropriate Element, L5 Tier 1 Spell of appropriate Element.
Exactly the same as the Tier 1 element, except add 10 TP to and subtract 40 Speed from each level. Also, the damage has a 1.5x multiplier attached. Tier 2 spells will thus do 50% more than either T1 or T3 spells to a single target.

Tier 3 Fire/Ice/Volt Spells:
Max Level: 5. Reqs: Same as Tier 2 Spell.
Area version of the Tier 1. There's only 5 levels, but each level is matched with an appropriate Tier 1 Level: L1 T3 = L1 T1, L2 T3 = L3 T1, L3 T3 = L5 T1, L4 T3 = L7 T1, L5 T3 = L9 T1. All damage stats are identical for the appropriate level, but expect to pay more than double the TP. L5 Tier 3 costs 52 TP, doing the same damage as a L9 Tier 1. 

Physics Spells:
Max Level: 5. Reqs: L1 Physics Up.
I've taken to call them Slasher, Crusher and Impaler. They're identical to Tier 3 spells except that you can get them a lot faster and they use the physical elements. TP cost and damage stats are identical, but remember that their Mastery level only goes up to 5 (for 106% damage) rather than 10 for the normal elements (111% damage).

Nuke:
Max Level: 5. Reqs: L10 TEC Boost, L5 Analysis.
Insanely powerful single target spell. Has no element and no Mastery Skill, but with an Attack of 180 at L5, you certainly won't notice a power deficiency. And like the T2 spells, it has a 1.5x damage multiplier. Insanely slow however (L1 Nuke is as slow as Landsknecht's and Gunners Charged Attacks, and L5 Nuke is only *slightly* faster than an L1 Tier 1/3 spell), and you need a lot of Skill Points to unlock this (20 skill points altogether compared to 10 for a Tier 2 - though Analysis is a worthy skill to get anyways, which is 15 of those 20 points required to unlock Nuke already).

Warp:
Max Level: 5. No Requirements.
Same as always, pretty much. TP lowering is more dramatic: it begins at a rather high 30, but drops rapidly, with the cost halving each level. TP cost at L5 is 1.

Chop:
Max Level: 5. No Requirements.
Nothing really to say about this.

Force Skill: Big Bang
Take L5 Nuke, make it area and even increase the Attack power a bit (200 compared to 180). Add high accuracy and speed, and you've got something that'll be doing an excessive amount of damage.

Skill Points/Retiring
You'll start with 3 Skill Points at L1, and gain 1 per level, just as in EO1. Your max level is 70. To start with.

Retiring at L70 brings in a L*30* apprentice with 40 skill points and +5 to STR, VIT, AGI, LUC and TEC. This new apprentice has a max level of L71.

Retiring this apprentice brings one with a new max level of L72 (no change in L30 stats from the previous apprentice though). This can continue on to L99, which is the true maximum. I don't know if there's any minimum level requirements to get the increase in max level, or whether it only goes up by 1 each time - the few tests I did were not enough to accurately judge this just yet.

Assuming stats don't get any other increases with more and higher retirements (they might do: I haven't managed to test this yet), the maximum stats should be:
L99, 109 skill points, 539 HP, 469 TP, 52 STR, 52 VIT, 68 AGI, 74 LUC, 102 TEC.

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Anyways, that's about all I plan on doing for a few days, but I hope this gives you a further insight in just how pervasive the balance changes are. 

Oh, right, a couple more things about Nuke. I forgot its TP Cost: 56 TP by L5, which makes it slightly more expensive than a Tier 3 spell, and almost twice as expensive as a Tier 2 spell. Also note that because it can't take advantage of elemental weaknesses, Masteries or Analysis, there are indeed times where the correct T2 spell will do much more damage. 

While I'm looking at Alchemist, here's what's *possibly* another bug to keep in mind: when calculating spell damage, the Attacker's VIT is one of the factors used to create the Target's Defense.

That means that the higher your VIT, the lower the damage your spells will do.

The difference isn't a huge amount - you'd need a lot of extra VIT to really notice anything... but it's worth keeping in mind. This only seems to affect spell-based damage, and I think only the Alchemist uses this particular formula out of the player classes.