babel-preset-es2015 está instalado e funciona bem com o recurso es6, como abaixolet a = 2;.
Mas não pode trabalhar com o recurso de módulos es6import fs from 'fs' como segue:

$ babel-node --presets es2015
> let a = 2;
'use strict'
> a
2
> import fs from 'fs';
SyntaxError: repl: Modules aren't supported in the REPL
import fs from 'fs';  
    at File.buildCodeFrameError (/usr/lib/node_modules/babel-cli/node_modules/babel-core/lib/transformation/file/index.js:407:15)
    at NodePath.buildCodeFrameError (/usr/lib/node_modules/babel-cli/node_modules/babel-traverse/lib/path/index.js:149:26)
    at PluginPass.ModuleDeclaration (/usr/lib/node_modules/babel-cli/lib/_babel-node.js:78:20)
    at newFn (/usr/lib/node_modules/babel-cli/node_modules/babel-traverse/lib/visitors.js:262:19)
    at NodePath._call (/usr/lib/node_modules/babel-cli/node_modules/babel-traverse/lib/path/context.js:63:18)
    at NodePath.call (/usr/lib/node_modules/babel-cli/node_modules/babel-traverse/lib/path/context.js:47:17)
    at NodePath.visit (/usr/lib/node_modules/babel-cli/node_modules/babel-traverse/lib/path/context.js:93:12)
    at TraversalContext.visitQueue (/usr/lib/node_modules/babel-cli/node_modules/babel-traverse/lib/context.js:152:16)
    at TraversalContext.visitMultiple (/usr/lib/node_modules/babel-cli/node_modules/babel-traverse/lib/context.js:110:17)
    at TraversalContext.visit (/usr/lib/node_modules/babel-cli/node_modules/babel-traverse/lib/context.js:182:19)

Então, oque há de errado?
Obrigado!