Limited companies are a "tax shelter" in that you pay less tax, but for only as long as the money stays in the company.
Paying money out of the company triggers personal taxes, as you realise.
If you weren't a company, you'd have paid 40% tax and loads of nic on it's profits etc (assuming more than £40-£45k p.a. profits). By trading through a company, the company has only paid 20% on those profits. When you draw them out, you personally pay more tax, i.e. so you end up back at the circa 40% level.
If you want to carry on trading through the company, but need more money out, then you'll just have to take the tax hit, which puts you back where you'd have been as a sole trader! If you want to close it down and either give up work or return to being an employee, you can close it down and draw out the reserves as capital gains tax with lower rate entreprenneurs relief tax rate, but doing that means you can't just phoenix and start another company again within 2 years.
I know it's hard to accept the tax hit, but you have to remind yourself that the low corporation tax rate was just a temporary tax shelter and you'll have saved a shedload of NIC anyway.
If you don't want to close it down, the best you can do is to plan your withdrawals sensibly over several years to level out your personal tax. I.e. drawing dividends of £50k per year is cheaper for tax than drawing out £150k in one year and nothing in the others.