What was objected to was that those particular open skies agrements (as was standard practice then) did not provide for an EU recognition clause and it is precisely on that ground that the Court of Justice found those agreements illegal under EU Law and had to be renegotiated (in the case of the US: replaced by an EU-wide agreement).

There is no general opposition of the Commission to bilateral agreements. The US was a special case. For the majority of states, however, it is still expected that agreements will be bilateral at Member State level rather than at EU level. What Member States must do, however, is include EU-recognition clauses to ensure that airlines from other Member States can exercise traffic rights under the agreement too even though in practice they are unlikely to use those rights. I would expect that the UK-Japan agreement is compliant on this point.

Far from being opposed to Open Skies agreements generally speaking, the Commission is rather favourable to them as it creates less problem from the perspective of EU recognition clauses. Under a stricter agreement than an Open Skies one, you could have issues with the designation of carriers entitled to fly the routes.