Sounds like you are getting your first taste of the world of a manager! I'm doing exactly the same thing 10 years later, with a much bigger budget and head count. So it never really ends.
I love the answer about doing some time estimates for each requested addition, and then sitting down all parties and working on a negotiation that gets the greatest degree of satisfication. I'm betting that since you are an intern, and many of the people you mention have seniority, that they will be able sort out amongst themselves who has the biggest stake and most power in the situation. But if not, don't hesitate to act as moderator -- after all, this is your project.
Other things to think about:
Types of stake holders:
- Customers - the person who controls the budget is often the most powerful of stakeholders, after all, they control your ability to do the work by controlling your funding. For an internal tool, this is probably an internal stakeholder, but it may be someone from a non-engineering group, if this tool is for a non-engineering purpose.
- Users - in the long run, users often make or break a tool. They definitely determine the tool's longetivity. It's not unusual, though, for users to lack advocates. And in a big internal project, it's entirely possible that users are not the customers.
- Technical Management - particularly when you are an intern and when you are working on an internal project, technical management is the group that's most important for you (as an individual) to please. They may have their own stake in the feature set, as they may be looking for a certain feature path for the product that fits a long term technological end game. Ideally, they should be on your side, and helping to figure out the best feature set.
In a big company, hopefully these roles are really well defined. Probably with an org chart. But not necessarily. And in a group that's used to working together, they may not make it really clear to a new comer exactly what the official roles are. As the guy doing the work, you're job should be to accurately and honestly tell them your best guess on what effort it will take to get the feature done. And to be open to ideas for making it cheaper/easier.
Negotiation:
The best negotiation advice I've ever gotten was "A good negotiation is one where everyone thinks they won". Sadly, the frequent outcome is that everyone feels equally screwed. The trick between every stakeholder leaving happy and every stakeholder feeling beaten down is to see the big picture and be innovative about getting everyone's needs met. In the end, no one really cares how you do it, if you can make their jobs easier, they will be happy. So finding features that serves everyone well can be the key to resolving the conflict.
Being able to do this well will really make a positive impact on your bosses. This is an extremely rare skill, and this type of finesse does get noticed.
Not having it does not mark you as a pariah, however, not many engineers enjoy negotiation. And it's never worth making every engineer be good at it. It's far better to find an engineering manager who is good at negotiating and to let them be the "speaker for the geeks", so the rest of the engineers can do their work in peace. :)