Assuming you're playing the US as am I. I've had great success against the IJN fleet. Here's what I suggest (much of which may already have been stated):
1) I Ramped all BB, CV, CL & DD tech to 1940 except for DD main guns which I stop at 1938. By that point, it's mid/late 1938 & time to start building any BB (optional) and CV fleets I want. I would NOT ramp hull size for BB or CV past 1940 (2.0 hull size) and you could even stop before that (1936/1938). Some may even not ramp hull size at all for BBs/CVs (1.6 default for US), but I like to have my capital ships a bit sturdier. I do suggest ramping it at least to 1938 (1.2 hull size) for DDs & CLs since the base models are pretty fragile (at least the DDs are). Continue to ramp AA guns since that's the one (other than radar) upgradeable item and you'll want the extra protection. You may not need to build anything other than transports/convoys/escorts past the first build up, but if you do plan more ships or just want to keep your tech somewhat current, I suggest engines - particularly DD & CL (not so much BB as you get little for it) and maybe BB/BC main guns.
2) From the start, also ramp naval tech which gives you bonuses to positioning and organization two or three levels. You might want to ramp a couple of levels into BB targeting chance as well. Also, there a couple of CAG techs worth ramping a bit before & during the war. You'll also want to ramp single engine fighter tech (torpedoes & light bombs as well) for the CAGs.
3) Positioning is key for naval gun ship fights. It determines whether you will hit the enemy ships...or your own! Ideally you'll have at least 90%, with 100%+ being the goal. Poor positioning will kill you - literally. I discovered that when I first played the game and sent in two or three BB fleets together into one naval battle. My positioning was under 50% and I did more damage to my own ships than the enemies LOL. Given your fleet hull penalties, if you're sending in two or more fleets into one battle (18-20+ ships), I bet your suffering a lot of friendly fire damage (and missing a lot of IJN ships in the process).
4) Per above, only attack with ONE fleet per province - the one exception (IMO) is when you have an amphibious invasion and you want BB shore fire, but only those two fleets (and hopefully you'll finish the invasion before getting attacked). Personally, I would not combine transports with anything else. They'll get damaged, but if your careful (rotate ships/fleets & repair), you won't lose more than a couple, if any. CV fleets should always be kept away from the fight. I like to keep one sea province of "space" between my CV fleets & the battle. Watch the enemy fleets little "green arrow" & reposition your fleets as it moves accordingly.
5) Organization is key for everything - including CAGs. Even if your BBs have 75-100% organization, if your DD escorts have little or none, none of your ships will fire (had that happen to me more than once). When your BB (or BC/CA) fleets have low organization it's time to head to port. Same for CAGs - once organization is low it's time for some CAG duty.
6) The CAG naval strike rules for FTM are VERY generous (only 2.5% stacking penalty - remember only naval strikes) so pile it on. You can attack with up to 20 CAGs per naval strike before the stacking rules work against you.
7) You have to follow through after the initial naval battle - you won't sink much (20 CAG naval strikes aside) in the first strike if the IJN fleet is unharmed at the start. So follow the IJN fleet and hit it again - just keep an eye on your gunships' & CAGs' strength/organization. If it's low, substitute with another gunship fleet or CAGs from another carrier (I use my old CV fleet as CAG backup for those cases). If all your fleets are dinged up, then head to port and wait for recovery before looking for new battles. Finally, worst case scenario (ex. you're fleet's damaged already and you get into an unexpected battle), you can always retreat if needed.
I built one new 3xBB + 4xDD fleet (for fun more than necessity) and two new 4xCV + 4xCL fleets starting in mid 1938 so everything would be ready by Oct 1941 at the latest. I also build another 6 transports before the start of the war. You might want to build 3-4 extra DDs as well since the old ones are pretty fragile. I put all three older US CVs with 5 of the "newer" CLs the US already has built. FWIW, next USA game I might try to build one more CV so all three CV fleets will have four carriers, or if I skip the BBs, then try to build another 4xCV + 4xCL fleet. For the old BBs, I use 3xBB + 1CA + 4-5xDD (old). The old BBs have low sea attack (for BBs) so the extra CA gives a little more punch to the fleet. I put the remaining old CAs & CLs together in two fleets, though frankly, I never use them (I really should find something to do with them). Transports are grouped into fleets of 5 or 6.
All the BB fleets have a fleet hull penalty of 4.0 (3.8 for the one with the Arkansas) which is more than offset by the tech I ramped and the fleet captains (I always use ones with a positioning bonus & ideally spotting bonus). The old CV fleet has a negligible fleet hull penalty (0.2%) though the new fleet does a hull penalty of 12. Still this is more than offset by the tech I've ramped and positioning isn't nearly as critical for CVs as it is with gun ships. All the other fleets have zero fleet hull penalties.
Edit: I forgot to add that as the war progressed, primarily after conquering Japan, I sunk quite a few ships via port strike. By that time the IJN fleet is culled quite a bit and what's left is damaged. Even if I can't see that a near by IJN port is occupied, I'll send in a few CAGs on a single day port strike to check it out. If there are ships there, I'll pummel away at them. I'll have a couple of BB fleets nearby if they try to escape so either way it's an easy win.