Firstly, if you are legally married, you can always choose to file jointly, as long as you agree, even if you filed separately last year.
Generally speaking, you pay more tax filing MFS (married filing separately) than MFJ, due to certain deductions and credits being limited or disallowed for MFS. As a result, the withholding tables calculate slightly higher withholding when filing separately. If you decide to file jointly, and don't change your withholding at all, you should probably expect a bit higher combined refund that you both received together last year. If you both change your withholding to married filing jointly, you will have too little tax taken out, because you will both get credit for the joint standard deduction, even though you can only take it once. The best way to calculate your withholding is to use this IRS calculator. Use it once for your combined finances, and file your W-4s based on the result.
https://www.irs.gov/individuals/tax-withholding-estimator
The student loan issue is more complicated. In general, if you have applied for income based repayment and you file MFJ, your payment will be based on your joint income. The only way to have your IBR payment calculated only on your income is to keep filing MFS. (If you are not using IBR, your payment is just fixed based on how much you borrowed and your interest rate, of course.)
The problem with filing MFS to get a lower payment is that the end game is uncertain. If your loan is not forgiven, then you just end up paying more over time. If your loan is forgiven, the amount that is forgiven is usually considered taxable income. So you could have a lower payment for 10 or 20 years, and then suddenly a huge tax bill when the loan is eventually forgiven. And in the mean time, you are paying higher taxes every year, due to the limitations of filing MFS. Those limitations become even more severe when you have children, because you can't qualify for the child care credit or EITC if you file MFS. And the chances of loans being forgiven in the future, and whether those forgiven loans will be taxable or tax-free, depends on future politics.
So, filing MFS to have a lower loan payment through IBR is a bet on the future political climate of the US. One way that things fall out is, you make smaller loan payments and eventually the balance is forgiven and you are free and clear. (You pay higher taxes along the way, but save in the long run.) The other way things could fall out is your loan is not forgiven and hangs over your head forever, or is forgiven but taxable, and you still paid higher taxes along the way.
There are probably financial advisors who can help with this. There's no one-size-fits-all answer.
