I operate a plane through a limited company. It is used for private and business, and is also rented out to a couple of other pilots.
I did a fair bit of research and this is a summary of what I found out:
The Revenue permits private use of a company asset if the private use is fully reimbursed. How "fully" is calculated is debatable but it needs to stand up to scrutiny. A market rate would be a good start. If you fully reimburse private use, you are not subject to the 20% benefit in kind business, and that AIUI is how syndicates that operate via a ltd co get around that problem; every pilot fully reimburses his usage to the company.
I could not find a problem with owning a plane in the same company which generates your livelihood, other than if there is an incident and the insurance refuses to pay out, your livelihood potentially goes down the pan. So a separate ltd co which operates the plane is a good idea.
The more flights are done by other pilots (i.e. rental) the more commercial the whole thing looks, which helps with both the Revenue and VAT. Obviously if the plane is rented out, you certainly do NOT want it owned by the main business, for obvious liability reasons.
According to recent reports, the Revenue has tried to charge BIK tax on large company assets which are nominally available to Directors to use - whether they are actually used or not. A booking system (i.e. the plane is not available unless previously booked) has been suggested by one of the major UK accountancy firms as a defence against this.
The best advice I can give is to find an accountant who has other clients in a similar situation. With so few GA pilots flying on business that won't be easy.
aiglon
The Revenue's view is that "other matters" do not include business use by the employee/director. Use by other employees or by the company itself (eg hiring it out to third parties) are "other matters".
The above would mean that a plane used solely for business by the sole owner of a business would be subject to BIK tax. That clearly isn't so. You can travel on business any way you choose (so long as it isn't way over the top) and a plane is a perfectly reasonable way to travel. People who have a plane owned by their firm and use it solely for business have the easiest case
AFAIK.