"It's not without issues" to me means I might object to parts of it but overall I'm positive, or I feel the issues can be accommodated, tolerated, or corrected.

"It's not without issues" to me means I might object to parts of it but overall I'm positive, or I feel the issues can be accommodated, tolerated, or corrected. "It has issues" is to me a stronger, more general objection to the whole thing.