the limited storage does seem intentional. Instead of using a little bit of MJ production to charge something for large bursts, I believe you should build you MJ production alongside your machines so that you can sustainably power them all when you need to and so that you can shut them off when you're done.
This seems to go against the point of boilers - but the point of boilers seems to be constant sustainable MJ powered automation where your assembly lines never shut off.
In a challenge, I've decided to forego boilers and run a bank of combustion engines from fuel. I have accumulated 36 engines on a bundled cable connected to several levers. Using the levers I can turn on any combination of engines 3 at a time up to the max of 36. When I am powering quarries I turn all 36 on at once and tesseract the energy to 3 simultaneously. When I am not powering quarries, I usually have 3 turned on just to run the pulverizers and such OR I have 12 turned on to run my assembly table or even 21 turned on to run my maga crucibles to melt lava.
The system works pretty well, and with pumps+tesseracts alongside railcraft tanks, fuel is plentiful and used efficiently. At max output, I use 36 buckets of fuel every 83 minutes and I am currently storing over 1000 buckets. I don't have to worry about constantly feeding a boiler and I can shut off the system when it's not in use.
You can kind of see the system here at 6:06
Ignore the rest of the video, it's something our admin made about a 1 week old player item duping. I would actually log on and take screenshots except the server is down for upgrades right now and I don't know if I'd be able to log on in the next day or so.
This way, MJ is stored in my fuel and not stored in the space inefficient redstone energy cells. I can store 600,000,000 MJ in my railcraft tank instead of using 1000 redstone energy cells.
I'd have to say though, if you are running constant lava melting, or want to have quarries running 100% of the time on say an automated frame machine, or are doing any other heavy automation heavy mj use then the boiler is the best tool for the job. At that point you should use a boiler of size closest to what you need to power everything 100% of the time and keep it running off a sustainable fuel source.