Most modern systems are "designed" for 28/29 inch wheels (that allow lower ratios), so going with a modern MTB groupset will introduce a risk of "running out of speeds". But in entry level ranges, there are limited numbers of alternatives.
With such bike, I would start from the 46/30 Acera Crankset (FC-MT210-2, with the matching FD-T3000 derailleur - hard to find — and a Deore M4100 shifter - much nicer to have a single lever shifter with a 2x).
For the rear, there are two options: if a 11-36 cassette suits your needs, it's possible to stay with Shimano (Alivio, M3100 series). If you need a higher range (with lower gears), there's the option of the Microshift Advent (11-42 cassette, long cage version required). Between the two options, the Microshift is the more "modern" one, and more expensive.
Otherwise, as Nathan mentioned, the new Shimano CUES seems very interesting, but is a few ranges higher in term of price and quality and is not widely available.
In 1x, larger cranks (40T) would be required to compensate for the smaller wheels. These are typically found now with road components, and frame clearance might be an issue.