I can see why the Council Legal Service would be ill at ease with the new Commission-Parliament Inter-Institutional Agreement. (The Legal Service Opinion about a draft version of this IIA is here.) While I would have to consider more carefully whether I think any specific provision actually violates the Treaties, it is certainly true that the whole thing breathes an air of Europhilia, without the Euroscepticism that the Council usually brings to the table. Without the reality check of a COREPER discussion, one would naturally expect the document to display a bias in the direction of treating the EP like a regular parliament, which indeed it does. Chapter II, for example, seeks to establish a relationship of ministerial responsibility between the Commission and the Parliament, even though it pays lip service to the fact that only the President of the Commission can dismiss an individual Commissioner. (par. 2-8 and 45-50). Similarly, the EP is to be involved in various ways in the negotiation of international agreements (par. 23-29 and Annex 3), in budgetary implementation (par. 30-31), in Commission meetings with experts (Annex 1), and in infringement suits against Member States (par. 44 and Annex II par 1.5).
On the whole, the Council Legal Service is certainly correct to remark that "[t]here is a clear lack of balance between the number of commitments made by the Commission to the European Parliament and the number of commitments made in turn by the latter" (fn. 5 of its opinion). On the other hand, virtually all the commitments contained in the IIA are either purely political, or at least political in their effects. I'm not sure that it is unlawful for the Commission to yield some of its political power to the Parliament. While the legal balance of powers is certainly enshrined in the Treaties, I'm not so sure that the political balance of powers is, too.
Finally, I'm content to see the European Parliament once again interested in implementation. While I was in Brussels, I had the great pleasure to attend a hearing on the topic organised by then-Green co-chair Monica Frassoni (cf. her EP profile here) in her capacity as a member of the JURI Committee, who seemed to have a refreshingly practical interest in wondering what happened to EU legislation after the EP was done with it. (Cf. the resulting rapport here.) Unfortunately, there is no proof that I was there, since I seem to have written Aidan Feeney's name on the attendance list (cf. the end of the minutes). What can I say, it was only the first month of my stage, so I didn't have the nerve yet to put down my own name. But I assure you that there is absolutely zero chance that the legendary Mr. Feeney was there, given that the hearing did not concern anything remotely codecision related.