If there are concerns with it overshadowing the Beast Master subclass, the DM can just say that it takes an action to command the animal to take the Attack, Dash, Disengage, Dodge, or Help action (or perhaps a subset of these options), but it requires a Wisdom (Animal Handling) check. Success means the animal does as commanded. Failure means it doesn't. If its owner is incapacitated or absent, as with the ranger's companion, it acts on its own, focusing on protecting its owner and itself.
By asking for an ability check here, it's less reliable than the beast master which doesn't require a roll to command the beast, and it doesn't get any of the other benefits a ranger's companion does. By costing an action to get it to, say, attack, it's probably worse than just making an attack oneself, except in particular situations where it makes the most sense (and will probably be awesome). This means it's probably best to keep them around because of its traits like Keen Hearing and Smell, as a pack animal, and sometimes to take a hit which might otherwise be directed at a PC. Occasional combat effectiveness and increased perception and carrying capacity for the party seems about right to me, especially considering the low cost of entry (e.g. a mastiff is only 25 gp which is cheaper than a 50-gp potion of healing and can effectively "heal" better if it takes a hit for a PC).