International trade agreements are so complex because no side wants to be exploited. That's why countries think very carefully about what kind of free trade to allow and what regulations apply. This sometimes means to make concessions: "You may underbid our domestic producers with this good, and in exchange you introduce our safety standards for producing that good so you can no longer underbid us on the world market".
When parts of an agreement are already implemented, those parts are already set in stone and are hard to re-negotiate (not without causing trouble for the companies which made business decisions based on these new regulations). That means the negotiators give up flexibility by pre-ratifiying parts of the agreement.
When there is news of a new trade agreement being negotiated, both industry and citizen lobbies will be on high alert. They will seek the opportunity to get their agenda into the agreement, or at least try to prevent the agreement from totally undermining it. All of them will approach the delegations and try to get their clauses in. Some of them will be successful, which will bloat the agreement text ("Yes, we start free-trading widgets, but only if we both make them without child labor and respect each others patents and produce them carbon-neutral and make them compatible with each others widget-holders").
You might remember the TTIP agreement which was designed with a lot of influence by industry lobbyists. The citizen lobbyists were not invited and reacted by rallying the European public against it.
When one of the parties to the agreement is a democratic country, then the negotiation delegation will not actually be authorized to agree to the agreement. They will have to pass it through the parliament first. It's usually easier to push one large free-trade bill through the legislative process than dozens. This is especially relevant for agreements with the EU, because these can usually be shot down by any of the parliaments of the member-states.
This was the situation last year when the regional parliament of Wallonia blocked the CETA agreement for a while. In this case the situation was resolved by the Belgian parliament overruling them. But if it would have been a national parliament, it wouldn't have been so easy. With piecemeal-introduced agreements, this problem would be worse, because each individual piece might be the one thing which is really bad for one single EU country and cause them to block it.