OK, so a reminder of principles first. Pensions allow you to avoid tax up front (the income tax you would have paid gets invested in the pension too), but it is taxable income when you later take the money out in retirement (you will pay income tax if total earnings in retirement are enough to pay it), whereas an ISA has no tax advantage up front, but is tax free to take out again. Both have tax-free growth. So money in a pension is not necessarily better than the same amount in an ISA. The disadvantage of a pension is that any money you put in you can't access until 55, but for you that's only 12 years a way so perhaps less of a concern than for somebody younger who might not want to commit to having their money tied up in a pension.
Auto enrolment versus SIPP:
I know the rules for regular employees and auto enrolment, the standard contributions are 4% employee, 3% employer and 1% from government in 20% tax relief for employee. And employers can offer to pay in more. However, as a partner of a company, I don't know if the regular rule is the same for you or whether directors and partners of companies may be exempt from auto enrolment rules - from a quick google search it looks like "yes" the rules are the same for you, but I'm not sure.
SIPP: you can pay contributions up to the annual allowance and get the tax relief, but no employer contributions.
You can of course have both auto enrolment and SIPP and pay into both, though if you have an auto enrolment scheme you could just choose to pay more than the 4% standard into that.
So, if you can have an auto enrolment pension, take it, because you get the employer contributions on top. However, if those contributions will come out of the profits of the company you jointly own, perhaps that is "your" money in a sense anyway, so it's only really saving the tax you would have paid on the company profits.
Longer term, the other consideration of auto enrolment versus SIPP is that auto enrolment schemes tend to be simple, but may have limited investments and may have higher fund % charges compared to a SIPP (some of the online SIPPs have a fixed platform fee and no fund charges, so once you have £25k or more invested you could save some money by paying a SIPP annual fee of around £100 a year but saving ~0.5% per year in fund fees). However, that is minor for now, and you can always transfer funds from one UK auto enrolment or SIPP pension to another, as and when you have enough invested that fund fee differences are significant. Fortunately, one of the requirements of Auto Enrolment schemes is that the fund charges are relatively low (capped at 0.67% a year or something) compared to historic pensions (fees could be up to 2% with service charges in addition).