If the ITD is going then there is no need to remove % bonus damage, don't give yourself the extra work where that's concerned. The major reason why ITD is important at the moment is actually due to HP values, those who have invested physical money or a great deal of time farming for moolah to buy the relevant accessories have greatly increased damage/hp/def etc which is where 'OP' classes and all that jazz come from. If someone is sittin with IV/V/VI cards for just stam/intel or w/e is obviously going to have much lower of the aforementioned stats hence them getting destroyed in 1 or 2 hits.
If you went to a BF before the 3rd job update you would see what I mean and I am sure you have went before and know what I mean. People who invested time and money in their gear dominated those who did not, before I spent money on my char I got 2 shot in DMs, once I invested £££ in my char that no longer happened and that is pretty much what it comes down to, also the use of trans cards and pots etc
The previous issues that were present only really applied to the Zerker and that was the class people complained about hence it's surge in popularity but even then only the donator Zerks could go around 2 shotting people and that was not everbody, only those who could not pvp or those who did not invest the same amount of £££ or time cold truly roflstomp. Mercenary class was strong but only a handful of us existed, Advents started creeping in popularity after their buffs, same applies to WLs, Magicians stayed roughly around the same in terms of how often they were played.
The biggest mistakes in the introduction of the 3rd update, in my opinion, are as follows;
The introduction of the imbued recipes and then the weapons they created further pushing the damage values higher than they were already causing both bugs to appear
The inclusion of other classes having ITDs, Wizards should not have one, the Sorcs ITD should have remained at 1 (Explosive Blast 2), Tanks ITD should have been removed as they are just that, Tanks, not damage dealers
% Bonus damage should not have been placed on ITD skills as it creates problems when players damage gets too high, having % bonus on non ITD skills is fine though and is a logical progression plus a nice attempt at working round the necessity of 3 classes having an ITD buff intrinsic to their way of playing. If you wanted to add some bonus damage then a low-mid fixed amount wouldn't cause any problems.
The above are not your fault though as you were pressured by people in the community who just whined about '3rd jobs not being here, I'm going to quit' and all that shite, that caused the problems Sedy, not you.
The only real problem people complained about before was the Berzerkers destruction and even then that was only an issue with certain people due to their high base damage values. I can guarantee you that some of those who complained about being stomped by the likes of a Zerker or Merc were the ones who did not compare gear wise and also used this to their own advantage when killing those who were poorly geared in comparison to them, but they did not complain then =). Funny thing is that the Glad has/had a similar skillset to the Zerker minus the CD reset and I only ever saw a handful of people as a glad in BFs and only 1 who could kill people but that was because he had thrown $$$ into his character and could stomp almost everybody.
BFs before the update actually had 3 or 4 people per team minimum during my nighttime, usually it was higher, now there are 4 people in an 85 DM/FM/BoA TOTAL, if we're fortunate enough to even have the BF load as people just don't go anymore. I think that speaks volumes as to the state of the game then and now. There are so many things in the game at the moment that cause characters (NOT classes) to be considered 'OP' and when the ITD is removed you will still have the same cries but from different people.
Make yourself 1 of each of the popular classes that are being played currently, gear it to a level that is feasibly possible in the game or simply examine those who are considered well geared and replicate their setup, take those characters to a lvl 85 DM, do a bit of pvp and test for yourself to understand better how things are working at the moment, better to get first hand experience than folks reporting to you their own biased opinion.
Edit: I still say ITD should be removed by the way, I'm just throwing caution to the wind for any further changes to the state of the game.